HTMLtools Documentation

File: ReferenceManual.html

Additional command subsets were developed for specialized conversions (JTVconvert, GenBatchScripts, and TestsIntersections) and may be ignored for routine Web page generation in other domains where they don't apply.

The JTVconvert commands can re-map data array names in Java TreeView mAdb data set files to more user friendly experiment names as well as generate HTML Web pages to launch these converted JTV files for each JTV data set.

The GenBatchScripts commands may be used to generate HTMLtools batch scripts for subsequent processing given a list of data test-results files to convert and a tab-delimited tests descriptions file. It is able to use a table (prepared with Excel or some other source) that describes this data and can then use that for extracting and inserting information from various mapping tables into the generated Web pages.

The TestsIntersections commands will synthesize a tests intersection summary table and Web page as well as generating some summary statistics. It uses the same data used in the GenBatchScripts commands.

The Converter GUI mode starts a graphical user command interface (GUI) where they can specify either individual parameter scripts or a batch file list of scripts to be executed in the background with the results shown in the user interface including the ability to view the generated HTML files though a pop up Web browser.

The Search GUI mode starts a database search graphical user interface (GUI) to generated a "flipped table" ((see examples Figure S.14 and Figure S.16)) on a subset of the data from a pre-computed edited table database. They can specify filters on the rows and columns (data and samples subsets), and presentation options to generate a HTML file though a pop up Web browser.

   1. Gather sets of laboratory experiments in multiple laboratories
   relating to the Jak-Stat gene pathway
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   2. Create Affymetrix microarray data (resulting in .CEL data files)
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   3. Create Inventory of relevant data and annotation of the data
   in the GSP-Inventory.xls spreadsheets consisting of:
   1) group arrays by experiment EG001, EG002,...EG00n;
   2) a top level spreadsheet ExperimentGroups describing 
   all EG experiments.
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   4. Consolidate data in mAdb (Microarray DataBase system 
   mAdb.nci.nih.gov). Data is uploaded to each EGxxx subproject, 
   and normalized by pooled RMA or MAS5.
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   4.1 Perform t-test or fold-change tests on subsets of the data 
   that makes sense to compare saving results (+ and - changes 
   separately) as gene subsets.
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   4.2 Export tab-delimited (Excel) mAdb Retrieval Reports (MRR) 
   for each gene set for 1) just the arrays used in the test; 
   2) all samples in the database.
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   4.3 Compute and export the hierarchical clustered heat maps as
   Java Tree View (JTV) .zip tab-delimited data sets for external 
   viewing for 1) just the arrays used in the test; 2) all samples
   in the database.   
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   5. Convert the MRR and JTV tab-delimited data to HTML Web pages
   using the HTMLtools tools
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   6. Merge links to this generated data with Web pages in
   the Jak-Stat Prospector Web server (and upload to the server).
   

Section 7 describes creating and running the scripts for the batchScripts/ directory for creating Web pages.

   1. Read the mAdb-TestsToDo.txt table that specifies all of the tests to
      be performed on subsets of the mAdb GSP database. For each test, these
      include: test name, samples being compared, test thresholds, test name
      and related annotation, tissue name, relative directory for the data
      (used both for input InputTree/ and output data Analyses/)
      generated directory trees.
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   2. Create lists of related tests by grouping by same tissue name.
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   3. Read additional mapping table files (ExperimentGroups.map, EGMAP.map,
      CellTypeTissue.map table to use in generating the summary web pages.
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   4. Create summary Web pages for each tissue type with links to Web pages
      for analyses we will generate and save in the Summary/ directory.
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   5. Generate all of the 'params .map' batch scripts, several for each test,
      and save them in the ParamScripts/ directory (see Figure 3 for 
      details). It then copies all support files (above mapping tables),
      JTVjars/, data.Table/ and other files required when running
      converter to generate Web pages. 
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   6. Generate a buildWebPages.doit file listing the params .map files to be
      processed with a subsequent batch run using the HTMLtools converter,
      and a Windows .BAT file, buildWebPages.bat
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   7. Start the buildWebPages.bat batch job which generates the Web pages in
      the Summary/, Analyses/ and JTV/ directory trees.  
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   8. Copy the generated Web pages to the Web server.
   

   
  tests (MRR & JTV) input:     Converter output:
  
  Tests for samples:
   {testName}+FC.txt           {testName}+FC.html 
                               {testName}+FC-keep.html      
   {testName}-FC.txt           {testName}+FC.html 
                               {testName}-FC-keep.html
           
  AND of above tests for ALL samples:
   {testName}+FC-ALL.txt       {testName}+FC-ALL.html
   {testName}-FC-ALL.txt       {testName}-FC-ALL.html
          
  JTV for test samples:        
   {testName}+FC-JTV.zip       {testName}+FC-JTV/ 
                               {testName}+FC-JTV.zip   
                               {testName}+FC-JTV.html  
   {testName}-FC-JTV.zip       {testName}-FC-JTV/ 
                               {testName}-FC-JTV.zip 
                               {testName}-FC-JTV.html
  
  JTV above for AND of above tests for ALL Samples:
   {testName}+FC-ALL-JTV.zip   {testName}+FC-ALL-JTV/ 
                               {testName}+FC-ALL-JTV.zip  
                               {testName}+FC-ALL-JTV.html 
   {testName}-FC-ALL-JTV.zip   {testName}-FC-ALL-JTV/ 
                               {testName}-FC-ALL-JTV.zip  
                               {testName}-FC-ALL-JTV.html  

   1. Edit the <GSP-Inventory Excel workbook to annotate the
      set of Affymetrix .CEL files where we assign the next
      free Experiment Group EGnnn, simple GSP ID, GSP ID, etc.
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   2. Upload the Affymetrix .CEL file data to the GSP mAdb 
      database and normalized the new samples using the pooled
      RMA data for the base GSP database.
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   3. Add new test to-do in the mAdb-TestsToDo.xls Excel workbook
      and upload the new test list to mAdb.
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   4. Run the batch tests in mAdb resulting in Excel and JTV
      data sets that are exported for conversion to Web pages.
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   5. Process these data using the HTMLtools converter
      into HTML pages and converted data for the Web server.     
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   6. Upload these Web pages and data to the NIDDK Jak-Stat 
      Prospector staging area for the jak-stat.nih.gov server.
   

1. First install Java (version 1.4 or later) on your computer if it is not already installed. You may install either the JDK or JRE.

2. Copy and unpack the HTMLtools-dist.zip file to a user directory where you want to convert files (or set up a temporary directory). There will be several sample data/ input directories, html/ directory, (JTVinput/, JTVjars/ and (optional) JTVoutput/ directories) as well as HTMLtools.jar and a sample param.map file in the data/ directory. You will also need to unpack the .BAT and .EXE files (described below in section 2.1 so they are executable. See Section 5 Data sets for examples of this data.

3. In the case of doing a Java TreeView conversion, there will be JTVinput/, JTVjars/, and (optional) JTVoutput/ directories. The zipped or unzipped mAdb JTV sub directories are put in JTVinput/ and the JTVjars/ has all of the .jar files needed to invoke JTV.

4. Then copy the tab-delimited .txt files you want to convert to the data/ directory relative to where the HTMLtools diretory resides. Alternatively, you could make a new data sub-directory in the HTMLtools directory (e.g., dataXXX or whatever you want to call it) since you may have any number of data directories in the HTMLtools directory. Edit a paramXXX.map file in the dataXXX/ directory modeled after one of the sample params .map files in the examples.

5. The converter may be started several different ways. The first two methods invoke graphical user interfaces. The third method involves typing commands into your operating system command. The fourth method involves invoking batch scripts (.BAT files in Windows) which basically supplies the command line you would have typed in the third method. The fourth method offers the most flexibility, whereas the first two are easier to use.

   a) Clicking on the supplied Java .jar file(s)

   If your computer (Windows, MacOS-X or Unix machines) is set up to execute Java .jar files, then you can run a Graphical User Interface version of the program by clicking on either:

   1. ConverterGui.jar to run the full converter. You select a parameter script (.map) file to excecute and then press the Process button. This is equivalent to running HTMLtools -gui. See the description Using the Graphical User Interface (GUI) to run the converter for more details.
   2. SearchGui.jar to run a subset of converter to specify a search query on a previously computed database file and then to generate a "flipped table" from the search results. You specify search terms and sample subsets and then press the Process button. This is equivalent to running HTMLtools -searchGui. See the description Search User Database with a Graphical User Interface (GUI) Generating Reports for more details.

   b) Typing commands to your operating system's command shell

   Start a command line window (e.g., run CMD in Windows, or create a shell window in Unix, MacOS-X, or Cygwin). The command line method requires that you know the switches to use and so is more difficult way to run the program. Note: you can specify the same switches you would type into the command line in a script file (describe next). Some of the required switches are:

        java -Xmx256M -classpath .;.\HTMLtools.jar \
             HTMLtools -inputDir:dataXXX -outputDir:html (etc.)  
      

   Using a parameter script file is easier. You can start the program through the command line Java as for example (in Windows):

        java -Xmx256M -classpath .;.\HTMLtools.jar \ 
             HTMLtools dataXXX/paramsXXX.map
   or (in Unix, MacOS-X, or Cygwin):
        java -Xmx256M -classpath .;./HTMLtools.jar \ 
             HTMLtools dataXXX/paramsXXX.map
   or
        java -Xmx256M -classpath . -jar HTMLtools.jar \ 
             dataXXX/paramsXXX.map
     

   where the dataXXX/ directory and the paramsXXX.map file are replaced by your data directory and params map file. Then, the generated HTML files will be in the html/ directory or whatever output directory is specified by the -outputDirectory switch in the paramsXXX.map file. This command line tells Java to run the program with 256 Mbytes of memory. For very large files, you may need to increase this memory size. For very large data sets, even that may cause problems and you may not be able to convert them since for the default mode, the Table is loaded into memory before being edited. Some commands such as -fastEditFile are designed to work with very large files and process them as a buffered I/O pipeline and so don't load the Table into memory.

   c) Run a "batch" script (.BAT in windows or the equalivalent in Unit.)

   In Windows, just click on one of the .bat files suplied (see the .BAT file scripts in demo-bat).

   Run the program through a command line Java as for example (in Windows):

6. The program generates (and overrides each time it is run) a HTMLtools.log file of the processing every time it is run. If the program is used in batch mode ('-batchProcess' switch), then all batch jobs process logging will be in the same logging file.

7. Batch processing, (with the -batchProcess switch), is performed on a list of params .map files contained in a batch input file (such as batchList.doit). It is invoked by

        java -Xmx256M -classpath .;.\HTMLtools.jar \
             HTMLtools -batchProcessing:batchList.doit  
      

8. The GenBatchScripts processing is performed in a special params script called data.GBS/params-genBatchScripts.map. There is nothing special about this script except that it uses the GenBatchScripts commands. So you could customize it for your data. It is invoked by

        java -Xmx256M -classpath .;.\HTMLtools.jar \
             HTMLtools data.GBS:params-genBatchScripts.map 
      

9. The program is documented in this file.

1. Change (cd) to the demo-bat directory where the .BAT files are distributed when you unpack the distribution .zip file.
2. Rename (this) RESTORE_BAT_FILES-bat file to the new name RESTORE_BAT_FILES.bat file so you can make it executable.
3. Execute the RESTORE_BAT_FILES.bat in the demo-bat directory to copy the other -bat files to .bat files in the distribution directory (the parent directory of demo-bat/) where they are now ready to run.

It is invoked from the command line as:
     java -Xmx512M -classpath .;.\HTMLtools.jar HTMLtools -gui

or using the M.S. Windows script (similar for Mac and Linux):
     cvtTxt2HTML-GUI.bat

Figure G.2

     java -Xmx256M -classpath . -jar searchGui.jar

     java -Xmx256M -classpath .;.\HTMLtools.jar HTMLtools -searchGui

You also need to select the set of samples to use by selecting one or more Experiment Groups (see the Jak-Stat Prospector Web site for details on Experiment Groups). In the 2. Select one or more 'Sample Experiment Groups' window, selecting ALL is the default and will select all 18 arrays. You can click on individual Experiment Groups. To select a range, click on the first one that starts the range and then hold the SHIFT key and click the end of the range. To select non-adjacent Experiment Groups, hold the CONTROL key as you select different groups. Pressing the Reset button, will clear these two windows.

You can save the text output generated during processing that is shown in the 3. Processing Report Log scrollable text area at the bottom of the window. Several File menu commands are used with this including: Clear Report-Log, and Save Report-Log As. Note that the Clear report, and Save report as commands are also available in the bottom as buttons with the same names.

You must specify a list of data search terms in the upper window 1. Enter list of Gene, Well ID or Probe ID.... The simplest way to specify these terms is to either cut and paste or type them into the window. To help demonstrate and simplify specifying the search terms, there are two commands in the File menu for setting the list: Set demo term-list data to enter a short list Stat5a Stat5b 1438470_at 1441476_at 1446085_at. The other is Import user term-list data from a file. The file can be a list of Genes or Feature IDs (probes) or Well IDs or any combination. Several example files are provided including data.search/LitRefGeneList.txt file, data.search/testGeneList.txt, and data.search/testFeatureIDList.txt. The first is a tab-delimited data with all 3 fields. The latter two examples just have lists of Genes or Feature IDs.

After you finish a search, you can do another one. The File menu options: Reset converter or the Reset button at the bottom of the Window will reset the search specification and make the Process button available.

The View menu offers additional some data input options. The menu Verbose reporting check box could be enabled it you want to see the details on the search and table generating as it progresses in the Report-Log window. When the search results table is being generated, you can modify it's presentation using other view options: Sort descending by column data in generated table (see Figure S.6 for more details). The Show data heat-map in View HTML to show the generated results table as a colored heatmap (see Figure S.14 for an example) This is the default. Finally, Set data precision for generated HTML to adjust the number of digits presented in the generated table (0 sets it to no fraction, whereas the default -1 shows the full precision of available in the data).

Adding fold-change statistics to the generated HTML report

SearcGUI Help

Three additional subsets of specialized commands that are described separately: the 3.1 GenBatchScripts commands, 3.2 Tests-Intersection and the 3.3 Java TreeView commands.

 {parameter command file}
                   [this argument does not start with '-' and is thus
                    assumed to be a parameter command file. It will then 
                    get all of the command switches from this file if 
                    present. Examples of command file contents are in 
                    the EXAMPLES section below. By convention, we name
                    these command text files 'paramXXX.map' with a '.map' 
                    file extension and keep them in the same directory
                    that we specify with -inputDirectory.  We refer to these
                    fileas throughout this document as "params .map" files.
                    The .map file extension is used for tab-delimited text
                    files that we do not want to convert. We only convert
                    tab-delimited text files with .txt file extensions.]

 -addE:{opt. epilogue file name}
                   ['-addEpilogue:{opt epilogue filename}' add an 
                    epilogue HTML file in inputDir or user directory
                    (common epilogue for all conversions). If the
                    keywords $$DATE$$ or $$INPUTFILENAME$$ is in the
                    file, it will substitute today's date or file name
                    respectively. $$FILE_ZIP_EXTENSION$$ will substitute
                    the file name with a ".zip" extension. Default name is 
                    'epilogue.html'. Default is to not add an epilogue to 
                    the HTML output.]
  
 -addO:{postfix name}
                   ['-addOutfilePostfix:{postfix name}' add a postfix
                    name to the output file before the .html. E.g., for
                    an output file 'abc.html', with a postfix name of 
                    '-xyz', the new name is 'abcxyz.html'. This can
                    be useful if you are mapping the same input file
                    by several different param.map files and saving
                    them all in the same html/ output directory.]

 -addP:{opt. prolog file name}
                   ['-addProlog:{opt. prolog file name}' to add a prolog 
                    HTML file in inputDir or user directory (common prolog 
                    for all conversions. If the keywords $$DATE$$ or
                    $$INPUTFILENAME$$ is in the file, it will 
                    substitute today's date or file name respectively.
                    $$FILE_ZIP_EXTENSION$$ will substitute the file name 
                    with a ".zip" extension. Default name is 'prolog.html'. 
                    The default is to not add a prolog to the HTML output.]

 -addRow
                   ['-addRowNumbers to preface each row with sequential
                   row numbers. Default is to not add row numbers.]

 -addT
                   ['-addTableName' to add TABLE name to HTML. Default 
                    is to not add the name.]

 -allowH
                   ['-allowHdrDups' to allow duplicate column fields 
                    in the header. Default is to not allow duplicates.]

 -alt:{color name}
                   ['-alternateRowBackgroundColor:{c}' alternate the
                    background row cell colors in the <TABLE>. 
                    Default is no color changes.]
          

 -batchP:{file of param specs, opt. new working dir}
                   ['-batchProcess:{file of param specs, opt. new working dir}'
                    batch process a list of param.map type files specified
                    in a file. If the {opt. new working dir}value is 
                    specified, it will change the current working directory 
                    of the HTMLtools when runnning -batchProcess so
                    that you can specify it run in a particular environment.
                    No other switches should be used with this as they will 
                    be ignored. If errors occur in any of the batch jobs, 
                    the errors are logged in the HTMLtools.log file 
                    and it aborts that particular job and continues on
                    to do the next job in the batch list. Default
                    is no batch processing.]

 -concat:{concatenatedDataFile,opt."noHTML"}
                   ['-concatTables:{concatenatedDataFile,opt."noHTML"}' to
                    create a new tab-delimited {concatenatedDataFile} (e.g., 
                    ".txt" or ".map" file) and a .html output file using the
                    base address (without the ".txt" or ".map" file extensions)
                    of the {concatenatedDataFile} and if the "noHTML" option
                    is not specified. The data is from the set of concatenated 
                    input text files data if-and-only-if they have exactly the 
                    same column header names. The -outputDir specifies where 
                    the files are saved. The input files are not converted
                    to HTML files. Default is to not concatinate the
                    input files. The -makeMapFile switch can be used
                    along with the concat switch to make a map file with fewer
                    columns.]                    
                    
 -copyFile:{sourceTreeDir,destDir}
                   ['-copyFile:{srcFile,destFile}' to copy an input source
                    file {srcFile} to a destination subdirectory {destDir}. 
                    There can be multiple instances of this option. Default is 
                    to not copy tree data.]                     
                    
 -copyTree:{sourceTreeDir,destDir} 
                   ['-copyTree:{srcTreeFiles,destPath}' to copy an input 
                     source tree subdirectory to a destination subdirectory. 
                     There can be multiple instances of this option. Default is
                     to not copy tree data.] 
                     
 -dataP:{nbr digits precision}'
                    [-dataPrecisionHTMLtable:{nbr digits precision}' sets the
                     precision to use in numeric data  for a generated HTML file.
                     The table must be a numeric data table (such as generated
                     using the '-flipTableByIndexMap' option. If the value is < 0, 
                     then use the full precision of the data (as supplied in the input 
                     string data). If {nbr digits precision} >= 0, then clip digits 
                     as required.]
                     
 -dirIndexHtml:{dir,'O'verride or 'N'ooverride}
                    ['-dirIndexHtml:{dir,'O'verrideor 'N'ooverride}' to create 
                    "index.html" files of all of the files in the specified directories 
                     in the list of directories specified with multiple copies
                     of this switch. It is useful when copying a set of directories
                     on a Web server that does not show the contents of the directory
                     if there is no index.html file. In addition, if the corresponding
                     flag'Override', then override the "index.html" file if it 
                     already exists in that directory otherwise don't generate the 
                     "index.html" file. Do this recursively on each directory.
                     Default is no index.html file generation. Multiple copies
                     of the switch are allowed.]

 -dropColumn:{column header name}
                   ['-dropColumn:{column header name}' to specify a 
                    column to drop from the ouput TABLE. There can be
                    multiple instances of this switch.]

 -exportB:{opt. big size threshold}
                   ['-exportBigCellsToHTMLfile:{opt. size for big}'
                    to save the contents of big cells as separate
                    HTML files with a prefix
                       'big-R<r>C<c>-<outputFileName>.
                    So for a (r,c) of (4,5) and a file name 'xyz.html',
                    the generated name would be 'big-R4C5-xyz.html'.
                    The big size threshold defaults to 200. Default is no
                    exporting of big cells.]

 -extractR:{colName,rowNbr,resourceTblFile,htmlStyle}
                   ['-extractRow:{colName,rowNbr,resourceTblFile,
                    htmlStyle}' to get and lookup a keyword in the
                    table being processed at (colName,rowNbr) and then
                    to search a resourceTblFile for that keyword. If
                    it found, then it will extract the header row and
                    the data row from the resource file and create
                    HTML of htmlStyle to insert into the epilogue.
                    If $$EXTRACT_ROW$$ is in the epilogue, then 
                    replace it with the generated HTML else insert
                    the HTML at the front of the epilogue. The
                    htmlStyles may be DL, OL, UL and TABLE. Default
                    is no row extraction.]
                    
 -fastE:{outTblFile}
                    ['-fastEditFile:{opt. output file} to allow processing
                     input file data line by line table that does not
                     buffer the data in a Table structure, but remaps each
                     line on the fly using -mapHdrNames,
                     {-dropColumns or -keepColumns} followed by 
                     -reorderColumns. Data is written immediately to an 
                     output stream so it can handle huge files. Because 
                     it is sequential, it can't do a -sortRowsByColumnData.
                     This would generally be used to generate a  tab-delim
                     .txt files that can be random accessed. HTML table
                     generation is disabled. It is used instead of 
                     '-saveEditedTable2File:{outTblFile,opt. "noHTML"}' 
                     and overides the -saveEditedTable2File options. 
                     Default is not to do a fast edit.]

 -files:{f1,f2,...,fn}
                   ['-files:{f1,f2,...,fn}' to specify list of files
                    here rather than all in all of the files in the 
                    inputDir. You can have multiple instances of this
                    switch.]
                    
 -flipA:{flipAclass}
                   ['-flipAclass:{flipAclass}' to specify the list of EG samples used
                    in class A if reporting the fold-change data in the flipped Table report.
                    Default is no list of EG samples is specified.]
                    
 -flipB:{flipBclass}
                   ['-flipBclass:{flipBclass}' to specify the list of EG samples used
                    in class B if reporting the fold-change data in the flipped Table report.
                    Default is no list of EG samples is specified.]
                                   
 -flipC:{flipColumnFile,flipColumnName} or -flipC:{*LIST*,flipColumnName,v1,v2,...vn} 
                   ['-flipColumnName:{flipColumnFile,flipColumnName}'
                    to specify the source Table column name to use in
                    filtering which row data to use in the 
                    '-flipTableByIndexMap' operation. An alternative specification
                    is '-flipColumnName:{*LIST*,flipColumnName,v1,v2,...vn}'
                    where the values are listed explicitly. Multiple instances
                    of this '-flipColumnName' switch are used to specify
                    the header entries by '{flipColumnName}' of the new 
                    flipped table. If the {flipColumnFile}' files exist,
                    they are used to filter the {flipDataFile} row entries.
                    Only the rows of the original Table that match one
                    of the {column-data-list} entries will be transposed.
                    Default is to transpose all rows unless the filter
                    files are specified.]                    
                     
 -flipD:{flipDirectory}
                   ['-flipDirectory:{flipDirectory}' to specify the directory to
                    save the generated flipped Table. Default is the data.search
                    directory.]                   
                     
 -flipE:{flipExcludeColumnName}
                   ['-flipExcludeColumnName:{flipExcludeColumnName}' to specify the
                    column names from the source Table exclude from the final flipped 
                    Table using the '-flipTableByIndexMap' operation. Multiple instances
                    of this switch are allowed. Default is to include all data Table 
                    columns unless the filter is specified.]                  
                       
 -flipO:{colHdrName1,colHdrName2,...,colHdrNameN}
                   ['-flipOrderHdrColNames:{colHdrName1,colHdrName2,...,colHdrNameN}' 
                    to specify the list of columns in the source Table that will be
                    used to create the flipped Table multi-line header entries.
                    This option must be specified when using the '-flipTableByIndexMap' 
                    operation.]  

 -flipRowF:{flipRowFilterNamesfile} or
 -flipRowF:{*LIST*,name1,name2,...,nameK}
                   ['-flipRowFilterNamesFile:{flipRowNamesFile}' or the alternate
                    '-flipRowFilterNamesFile:{*LIST*,name1,name2,...,nameK}'switch specifies
                    the source Table column names to use in filtering which source sample 
                    columns data will be used as rows in the finalflipped Table using the 
                    '-flipTableByIndexMap' operation. Analternative specification is 
                    '-flipRowFilterNamesFile:{*LIST*,name1,name2,...,nameK}' where the values
                    are listed explicitly. If the "*LIST*" name is used instead of the file
                    name, then the rest of the switch specifies the row names. Only the 
                    columns of the original Table that partially match one the 
                    {flipRowNamesFile} entries will be transposed. Default is to transpose 
                    all data Table columns unless the filter is specified.]

 -flipRowGSP:{list of filter substrings}
                   ['-flipRowGSPIDfilters:{list of filter substrings}' is an optiona         
                    list of substring filters used to filter Experiment Group sample name
                    rows in the flipped table computation when using the
                    '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile}' switch. It matches
                    case-independent substrings in the GSP ID names for the samples where
                    if more than one substring is specified, then they must all be found
                    for that sample to be used (e.g., ".Stat .GH" requires a ".Stat" and
                    a ".GH" to be present). Default is no filtering.] 
                    
 -flipSa:{flipSaveOutputFile}
                   ['-flipSaveOutputFile:{flipSaveOutputFile}' is the alternate 
                    output (HTML and TXT) file name to use when generating the 
                    flipped Table using the 
                    '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
                    switch. Default is to generate the output file name from the
                    input file base name, adding a postfix using the
                    '-addOutfilePostfix:{postfix name}' or "-flipped" default
                    postfix. If the switch is not specified, it will use the base 
                    input file name. (See Example 14
                    for an example of it's usage.) ]
                    
 -flipT:{flipDataFile,flipIndexMapFile,(opt)maxRows}
                   ['-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
                    to generate a transposed file using random access file indexing to 
                    create a multi-line header (1 line for each column name in the 
                    list) using the list of columns previously specified with the 
                    -flipColTableList and -flipRowTableList filters. It uses the index-map
                    created with '-makeIndexMapFile:{colName1,colName2,...,colNameN}'
                    command. It analyze the index map Table and then uses 
                    all columns before the ("StartByte", "EndByte") columns
                    to define the flipped Table header. See the '-flipColTableList' and 
                    -flipRowTableList to restrict which flipped column data to use. 
                    See the '-flipRowTableList' to restrict which flipped row data to 
                    use. Default is to not flip the Table.]                   
                                              
 -flipU:{colHdrName1,colHdrName2,...,colHdrNameN}
                   ['-flipUseExactColumnNameMatch:{TRUE | FALSE}' to specify the exact 
                    match filter flag. If an exact match, then match '-flipColumnName:{names}'
                    exactly, otherwise do look for substring matches. Ignore case in
                    both instances. This option may be specified when using the 
                    '-flipTableByIndexMap' operation. The default if no 
                    flipUseExactColumnNameMatch is specified is "AND".]            

 -font:{-1,-2,-3,-4,+1,+2,+3,+4}
                   ['-fontSizeHtml:{font Size modifier}' to change
                     the <TABLE> FONT SIZE in the HTML file.]
                     
 -gui
                   ['-gui' to invoke the graphical user interface version
                    of the converter. See 
                    Using the Graphical User Interface (GUI) to run the converter.] 
                            
 -hdrL:{n}
                   ['-hdrLines:n' to include in header. The last line
                    row is the one searched for mapping column URLs.
                    Default is 1 line.]                  
                    
 -hdrM:{oldHdrColName,newHdrColName}
                   ['-hdrMapName:{oldHdrColName,newHdrColName}' to map
                    an old header column name {oldHdrColName} to a new
                    name {newHdrColName}. There may be multiple instances
                    of this switch. Default is to not do any mappings.]

 -joinT:{joinTableFile}
                    ['-joinTableFile:{joinTableFile}' adds the contents of 
                     the {joinTableFile} file to the table being processed. 
                     This allows us to add fields that can be used for 
                     sorting the new table by the {joinTableFile} data
                     if it is defined. This switch can not be used with 
                     the -fastEditFile option. Default is not to join
                     any tables.]

 -keepColumn:{colName}
                   ['-keepColumn:{colName}' specifies which columns
                    to keep in multiple instances of the switch.
                    Then, when the Table is processed, it drops all
                    columns not listed. It may be used as an 
                    alternative to -dropColumn as the Table may have
                    unknown column names. Default is not active.]

 -help (or '?')
                   [print instructions to see the README.txt file.]

 -hrefD:{colName,Url,mapToken}
                   ['-hrefData:{colHdrName,Url,(optional)mapToken}' to
                    get the mapping of column header name and the Url to use 
                    as a base link to use for making a URL for Table data
                    in that column. It makes the URL by appending the data 
                    in cells in that column to the Url. ([TODO] If 
                    the optional mapToken is specified, then replace the cell 
                    contents for the occurance of the mapToken in Url.) 
                    There can be multiple instances of this switch. See
                    the following switch '-hrefHeaderRow' to change the mapping
                    from Table data to header rows. ]
 -hrefHeaderRow
                   ['-hrefHeaderRowMapping' is used with the above switch
                    '-hrefData:{colHdrName,Url,(optional)mapToken}' to map
                    the data in the header row(s) instead of the data in 
                    the Table data columns. It searches the first column of
                    the header rows to find the colHdrName to determine 
                    the row to be mapped to that colHdrName. Unlike the
                    -hrefData option, the colHdrName can be embedded within  
                    a string. The default is not to map the header rows.]

 -inputD:{input directory}
                   ['-inputDirectory:{input dir}' where the input 
                    tab-delimited table .txt files to be converted are
                    found. By convention, we name other text files that 
                    we may need, and want to keep in the inputDirectory 
                    but do not want to convert to HTML, with a '.map' 
                    file extension. Examples of non-data files include 
                    'paramXXX.map', 'prolog.html', 'epilogue.html', etc., 
                    Default directory is 'data/'.]
                    
 -limitM:{maxNbrRows,(opt.)sortFirstByColName,(opt.)'A'scending or 'D'escending}
                   ['-limitMaxTableRows:{maxNbrRows,(opt.)sortFirstByColName},
                    (opt.)'A'scending or 'D'escending}' to limit the number of 
                    rows of a table to {maxNbrRows}. If the {sortFirstByColName}
                    is specified, then sort the table first before limit the 
                    number of rows. Default is  not to limit rows.]

 -log:{new log file name}
                   ['-logName:{new log file name}' to log all 
                   information about the processing to the console and
                   then to save this output in a log file. The new file
                   must end in ".log". Default is to use the 
                   "HTMLtools.log" file name.]
                                   
 -makeI:{colName1,colName2,...,colNameN}
                   ['-makeIndexMapFile:{colName1,colName2,...,colNameN}' to
                    make an index map Table file (same name as the input file
                    but with an .idx file extension) of the input file (or the
                    file output from -saveEditedTable2File after the input 
                    table has been edited). The index file will contain the
                    specified columns in the column-list followed by the 
                    StartByte, EndByte for data in the input table with those
                    column values. This file can then be used to quickly 
                    index a huge input file probably using a Hash table of 
                    the selected column names instances to lookup the 
                    (start,end) file byte pointers to random access the 
                    large file. The software to use the index file is not
                    part of HTMLtools at this time.
                    The default is not to make an index map file.]

 -makeM:{makeMapTblFileName,orderedCommaColumnList}
                   ['-makeMapFile:{makeMapTblFileName,orderedCommaColList}'
                    used with -concatTable command to also make a map
                    file at the same time. This switch is only used
                    with -concatTable. Default is no map is made.]

 -makeP
                   ['-makePrefaceHTML' to make a separate preface
                    HTML file from the input text proceeding the table
                    data. The file has the same name, but has a
                    "preface-" added to the front of the file name. The 
                    first generated HTML file is then linked from the 
                    second generated file. Default no preface file.]
      
 -makeS              
                    ['-makeStatisticsIndexMapFile' to make a 'Statistics Index Map' 
                     table file with the same base file name as the index map (.idx) 
                     but with a .sidx file extension. It is invoked after the 
                     IndexMap file is created (using the '-makeIndexMapFile' switch).
                     Therefore, it must be specified in a subsequent command line 
                     (if using batch). Default is not to make a Statistics Index Map.]

 -mapD:{$$keyword$$,toString}
                   ['-mapDollarsigns:{$$keyword$$,toString}' to 
                    map cell data of the form '$${keyword}$$' to
                    {toString}. The preface, epilogue as well as the
                    table cell data is checked to see if any keywords
                    should be mapped. There may be multiple instances
                    of this switch. Default is to not do any mappings.]

 -mapH:{mapHdrNamesFile,fromHdrName,toHdrName}
                   ['-mapHdrNames:{mapHdrNamesFile,fromHdrName,toHdrName}
                    to map header names. E.g., map long to short header 
                    names, or map obscure to well-defined header names. 
                    The map file (specified with a relative path) is a 
                    tab-delimited and must contain both the {fromHdrName} 
                    and {toHdrName} entries. Default is no mapping.]

 -mapO
                   ['-mapOptionsList' to map ;; delimited strings 
                    to inactive <OPTION> pull-down option lists.
                    Default is no mapping to option lists.]

 -mapQ
                   ['-mapQuestionmarks:{??keyword??,toString}' to 
                    map cell data of the form '??{keyword}??' to
                    {toString}. If the toString is BOLD_RED,
                    BOLD_GREEN, or BOLD_BLUE, then just map the
                    all ??{keyword}?? string to bold and red (green,
                    or blue). The preface, epilogue as well as the
                    table cell data is checked to see if any keywords
                    should be mapped. There may be multiple instances
                    of this switch. Default is to not do any mappings.]

 -noB
                   ['-noBorder' to set no border for tables. The
                    default is there is a 'BORDER=1' in the TABLE.]

 -noHeader
                   ['-noHeader' set no header for tables. The 
                    default is there is a header in input file.]
                    
 -noHTML
                   ['-noHTML' set to not generate HTML if it would
                    normally do so. This switch disallows generation of
                    HTML when doing a input file processing if that 
                    operation also allows HTML generation. This is useful
                    if doing editing of large input files to generate 
                    index maps or saved files. The default is to allow
                    the generation of HTML..]

 -outputD:{output directory}
                   ['-outputDirectory:{output directory}' to set the 
                    output directory.  The default directory is 'html/'.]

 -reorderC:{colName,newColNbr}
                   ['-reorderColumn:{colName,newColNbr}' to reorder
                    this column to the new column number. You may
                    specify multiple new columns (they must be
                    different). Those columns not specified are moved
                    toward the right. This is done after the list of
                    dropped columns has been processed. There can be
                    multiple instances of this switch. Default is not
                    to reorder columns.]

 -reorderR
                   ['-reorderRemainingColumnsAlphabeticly' used if doing
                    a set of -reorderColumn operations, sort the remaining 
                    columns not specified, but that are used, alphabetically.
                    Default is not to sort the remaining columns.]

 -rmvT
                   ['-rmvTrailingBlankRowsAndColumns' in the table.
                    Default is not to remove trailing blank lines or
                    trailing blank columns.]
                    
 -saveE:{outTblFile,opt. "HTML"}
                    ['-saveEditedTable2File:{outTblFile,opt. "HTML"}'
                     to make a Table file from the modified input 
                     table stream. It is created after the Table is
                     edited by -dropColumns, -keepColumns, 
                     -reorderColumns, -sortRowsByColumn. If the outTblFile
                     is not specified (i.e., ":,") then the input file name
                     with the name from the input file with the postfile
                     name from the '-addOutfilePostfix:{postfix name}' is 
                     used. If the "HTML" option is set, it also outputs the 
                     HTML when doing this operation. Note that the switch
                     should not be used with '-fastEditFile:{opt. output file}'
                     which can be used for converting very large files
                     without generating the HTML file. Default is not to save 
                     the Table.]
                     
 -searchGui
                   ['-searchGui' to invoke the graphical user interface for the
                    database search engine to generate a flip table. See 
                    Search Database GUI generating specialized reports. 
                    Also see Example-17
                    for examples of the default parameter file used as the
                    basis of the flip table generated. Default is no search GUI.]                             

 -shrinkB:{opt. size for big,opt. font size decrement}
                   ['-shrinkBigCells:{opt. size for big,opt. font size
                    decrement}' in the Table with more than the big
                    threshold number of characters/cell by decreasing
                    the font size to -5 (or the opt. font size 
                    decrement) for those cells. The big size threshold
                    defaults to 25 characters. Setting the threshold to
                    1 forces all cells to shrink. Default is not to
                    shrink cells.]
                    
 -showDataHeatmapFlipTable
                   ['-showDataHeatmapFlipTable' used to generate colored heat-map
                    data cells in a HTML conversion for a flip table using the 
                    '-flipTableByIndexMap' option. It uses the global statistics 
                    on the (digital) data in the Statistics Index Map .sidx file 
                    if it exists to normalize the data and generate a cell color 
                    background range in 7 quantiles of colors: dark green, 
                    medium green, light green, white, light red, medium red, dark red. 
                    Default is not to generate the colored heatmap.]
                    
 -sortFlip:{col data name}
                   ['-sortFlipTableByColumnName:{col data name}' specifies the name 
                    of field in the flip table to use in sorting by column data in 
                    descending order in the generated table. It is used with the 
                    '-flipTableByIndexMap' option. Note this name can be any of the 
                    flipped header column  values (multiheader data names}. When doing
                    the sort it matches  the specified name with any of the header 
                    rows to find the column to use for the sort. Default is not to
                    sort the generated flip table.]

 -sortR:{colName,'A'scending or 'D'escending}
                   ['-sortRowsByColumn:{colName,'A'scending or specified column. 
                    You can specify 'Ascending' or 'D'escending. This is done after
                    any columns have been dropped or reordered. Default is not to
                    sort columns. If the column is not found, don't sort - just 
                    continue. You can have multiple instances of the switches. If the 
                    first column name is not found, it looks for the second, etc.
                    and only ignores the sort if no column names are found. Default 
                    is not to sort the table.]
                    
 '-startT:{keyword}
                   ['-startTableAtKeywordLine:{keyword} specifies the start
                    of the last line of a Table header by a keyword that
                    is part of any of the fields in that line. This is
                    useful when reading a file with complex preface info
                    with possibly multiple blank lines. It can be used
                    with the '-hdrLines' switch to specify multiple
                    header lines. Default no keyword search.]                    
                   
 -tableD:{tablesDirectory}'
                   ['-tableDir:{tablesDirectory}' to set the various mapping
                     tables directory. These tables are used during various
                     conversion procedures. They include both the .txt and
                     the .map file (same file, but with different extensions).
                     Examples include: EGMAP.map(.txt), ExperimentGroups.map(.txt)
                     mAdbArraySummary.map(.txt). The default directory is 
                     'data.Table/'.]
                    
 -useOnly
                   ['-useOnlyLastHeaderLine' to reduce the number of header 
                    lines to 1 even if there are more than 1 header line.
                    Default is to use all of the header lines.]
 

Section 7 describes creating and running the scripts for the batchScripts/ directory for creating Web pages.

The parameters specify the data used in the output files generation include several directories in the batchScripts/ directory:

• batchScripts/ParamScripts/ - contains the GenBatchScript's generated params .map files that will be used in the subsequent conversion batch run.
• batchScripts/inputTree/ - contains tab-delimited .txt input files in the same directory structure as that defined in the test-ToDo-list Table.
• batchScripts/Summary/ - contains the subsequent HTML summary Web page files in the same relative directory structure as that defined in the test-ToDo-list Table.
• batchScripts/Analysis/ - contains the subsequent HTML test Web page files generated when the batch script is run. Data is in the same relative directory structure as that defined in the test-ToDo-list Table.
• batchScripts/JTV/ - contains the subsequent JTV and their HTML test Web page files generated when the batch script is run. Data is in the same relative directory structure as that defined in the test-ToDo-list Table.
• batchScripts/JTVjars/ - contains the JTV jar files required to support the Java TreeView at run time.
• batchScripts/data.Table/ - contains the mapping tables required to support processing the buildWebPages.doit batch processing.

Additional data files are used when the -genBatchScripts command is run including:

• data.Table/EGMAP.map - to map long to short header names
• data.Table/ExperimentGroups.map - to be a resource for Expression Group data
• data.Table/CellTypeTissue.map - contains the Introductions used in the Summary Web page generation.
• data.Table/mAdbArraySummary.map - contains the table required for SGID mapping of JTV files.
• Prolog template HTML files (prologMRR.html and prologJTV.html) used when the params .map scripts are run are run using the subsequent batchScripts/buildWebPages.bat processing.
• Epilogue template HTML files (epilogueMRR.html and epilogueJTV.html) used when the params .map scripts are run using the subsequent batchScripts/buildWebPages.bat processing.
• Summary template HTML files (SumaryProlog.html, SummaryExperimental.html, SummaryAnalysis.html, SummaryFurtherAnalysis.html, SummaryEpilogue.html) used when generating the Summary HTML Web pages for each tissue. These are saved in batchScripts/Summary/.
• Params .map template files used when generating the specific params .map files for the subsequent batch run. These include (paramsTemplate-MRR.map, paramsTemplate-MRR-keep.map, paramsTemplate-JTV.map,paramsTemplate-JTV-ReZip.map, and paramsTemplate-MRR-saveFile.map). The generated params .map files are saved in batchScripts/ParamScripts/.

There may be multiple instances of the -genCopySupportFile, -genParamTemplate, -genSummaryTemplate switches.

                        
 -genBatch:{batchDir,paramScriptsDir,inputTreeDir,summaryDir,analysisDir}' 
                   ['-genBatchScripts:{batchDir,paramScriptsDir,inputTreeDir,
                    outputTreeDir,analysisTreeDir,JTVDir}' to generate a set 
                    of scripts to batch convert a set of tab-delimited Table
                    test data files specified by the -genTestFile:{testToDoFile}
                    Table in the {batchDir} directory. It generates a set of 
                    parameter .map files in the {paramScriptsDir} directory. It
                    also generates a set of summary HTML Web pages in {summaryDir}
                    that describe the data, one page for each type of tissue, 
                    and (pre) generates links to data that will be generated in
                    the {analysisTreeDir} when the batch script is subsequently 
                    run. These new params .map files can then be run by a converter
                    batch file called buildWebPages.doit started with a 
                    Windows buildWebPages.bat BAT file to start the batch
                    job (both files are in the batchDir directory along with a 
                    copy of HTMLtools.jar). The buildWebPages.bat file
                    could easily be edited to run on MacOS-X or Linux. The paths 
                    created in the {inputTreeDir}, and {analysisTreeDir} base paths
                    use the "Relative Directory" data in the {testToDoFile} within
                    those directories. This generated batch .doit script will
                    process a data set to generate a set of HTML pages and 
                    converted database .txt files defined by the {testToDoFile}
                    Table database. Default is no batch script generation. 
                    Additional switches required with -genBatchScripts are:
                    -genTestFile, -genMapEGdetails, and -genMapEGintroduction]

 -genC:{support file}
                   ['-genCopySupportFile:{support file}' to specify a list
                    of support files to copy to the output batchDir (e.g., 
                    '-outputDir:batchScripts'). The support files are 
                    specified with a list created using multiple instances of 
                    -genCopySupportFile:{support file}. Default is no support
                    files to copy.]                    
                     
 -genMapEGd:{EGdetailsMapFile}
                   ['-genMapEGdetails:{EGdetailsMapFile}' specifies the 
                    'details' Table used when the -genBatchScripts switch is 
                    invoked. This is required when the -genBatchScripts switch
                    is used.] 
                    
 -genMapIntro:{introductionMapFile}
                   ['-genMapIntroduction:{introductionMapFile}' specifies the 
                    'Introduction' Table used when the -genBatchScripts switch
                    is invoked. This is required when the -genBatchScripts 
                    switch is used.]
                    
 -genP:{name,paramTemplateFileName}
                    ['-genParamTemplate:{name,paramTemplateFileName}' to
                    specify a list of parameter map Templates that are used 
                    for mapping the test-ToDo-list data so that (param-MRR, 
                    param-MRR-keep, param-JTV) etc. dynamically.  These are 
                    then mapped into the following keywords that may appear in
                    any of these templates: $$TISSUE$$, "$$TEST_NAME$$", 
                    "$$MRR_FILE$$", $$DESCRIPTION$$, $$PROLOG$$, $$EPILOG$$, 
                    $$DATE$$. Multiple unique instances are allowed. The
                    default is no parameter templates.]
   
 -genS:{orderNbr,templateFileName}               
                   ['-genSummaryTemplate:{orderNbr,templateFileName}' to define
                    a list of Summary Templates that are used for mapping the
                    test-ToDo-list data so that (summaryProlog, summaryExperimental,
                    summaryAnalysis, summaryFurtherAnalysis, summaryEpilogue) 
                    etc. dynamically. Set by -genSummaryTemplate:{orderNbr,
                    templateFileName} instances that can be used to generalized 
                    the currently hardwired. These are then mapped into the 
                    following keywords that may appear in any of these templates: 
                    $$TISSUE$$, $$LIST_EXPR_GROUPS$$, $$DESCRIPTION$$, 
                    $$ANALYSIS$$, $$FURTHERANALYSIS$$, $$DATE$$. The 
                    $$INTRODUCTION$$ is extracted from the {"CellTypeTissue.map"}.
                    Default is no templates being defined. Multiple instances
                    are allowed where they are concatenenated by the orderNbr
                    associated with each template.] 
 
 -genTest:{testToDoFile}
                   ['-genTestFile:{testToDoFile}' specifies the tests to do
                    when the -genBatchScripts switch is invoked. This is 
                    required when the -genBatchScripts switch is used.]  
                     
 -genTree:{sourceTreeDir,destDir}
                   ['-genTreeCopyData:{sourceTreeDir,destDir}' to copy an
                    input data tree data to batch scripts subdirectory.
                    There can be multiple instances of this option.
                    Default is to not copy tree data.]                 

                  
 -addFCranges
                   ['-addFCrangesForTestsIntersectionTable' may be used when 
                    generating a table Tests-Intersection Table using the 
                    '-makeTestsIntersectionTbl:{testsToDoFile}'. This switch
                    does a simple fold-change (FC) row analysis after the
                    Tests-Intersection Table is created by adding ("Min FC" 
                    "Max FC" "FC Range") data for each row. Because this
                    extends the table, you can sort by any of these fields.]                    
                    
 -addRange
                   ['-addRangeOfMeansToTItable' to add the ("Range Mean A", 
                    "Range Mean B" and "FC counts %") computations to an expanded
                    Tests-Intersection Table table. Default is to not add these 
                    fields.]
                                                            
 -filterData:{dataTableField,d1,d2,...,dn}
                   ['-filterDataTestIntersection:{dataTableField,d1,d2,...,dn}' that
                    is used with the '-makeTestsIntersectionTbl:{testsToDoFile}' to
                    filter the MRR rows using the  specified MRR {dataTableField}
                    and use it if it matches any of {d1,d2,...,dn} substrings.
                    The default is not to filter the Tests-Intersection Table.]
                                        
 -filterTest:{testTableField,d1,d2,...,dn}
                   ['-filterDataTestIntersection:{testTableField,d1,d2,...,dn}' that
                    is used with the '-makeTestsIntersectionTbl:{testsToDoFile}' to
                    filter the Tests-ToDo table rows using the specified {testTableField}
                    and use it if it matches any of {d1,d2,...,dn} substrings.
                    The default is not to filter the Tests-Intersection Table.]
                    
 -makeT:{testsToDoFile,testsInputTreeDir}
                   ['-makeTestsIntersectionTbl:{testsToDoFile}' that
                    generates a table Tests-Intersection Table that contains
                    data from the individual tests from the tests input data tree
                    specified by the tests in -tableDir directory in the
                    {testsToDoFile} which specifies the relative data file tree.
                    The tree is found in -inputDir directory. The data files in 
                    the tree are used as input data. The computed table is 
                    organized by rows of +FC genes/Feature-IDs and -FC 
                    genes/Feature-IDs. The data from the {testsToDoFile} is used 
                    to get additional information for each test as follows.
                    This switch is used with the '-noHTML' and/or '-saveTable'
                    switches. If HTML is generated, then the '-addProlog' and
                    '-addEpilogue', '-mapQuestion', and '-mapDollar' can be used.
                    You can filter the MRR rows using the 
                    '-filterDataTestIntersection:{dataTableField,d1,d2,...,dn}' and
                    the {testsToDoFile} test data using the                     
                    '-filterTestTestIntersection:{testTableField,d1,d2,...,dn}'.
                    The default is not to make the Tests-Intersection Table. You
                    can do a simple FC row analysis by adding ("Min FC" "Max FC"
                    "FC Range") for each row using the
                    '-addFCrangesForTestsIntersectionTable' switch.]

Reorder:
  "WID:... || xxxxxx_at || MAP:... || gene -- geneDescr. || RID:..."
to
  "gene -- geneDescr. || xxxxxx_at || WID:... ||  MAP:... || RID:..."

 
 -jvtB:{button name for JTV activation button}
                   ['jvtButtonName:{button name for JTV activation button}' 
                    that may be used with '-jtvHTMLgenerate' to label the 
                    button to activate Java TreeView. The default is 
                    "Press the button to activate JTV".]

 -jtvC:{JTV jars directory}
                   ['-jtvCopyJTVjars:{JTV jars directory}' to copy the 
                    JTV jar files and plugins to the jtvOutputDir. 
                    The default is no copying of the .jar files.]

 -jvtD:{description text for prologue}
                   ['-jvtDescription:{description text for prologue}' 
                    that may be used with '-jtvHTMLgenerate' to insert 
                    additional text into the prolog where it replaces 
                    $$DATA_DESCRIPTION$$. The default is no description.]                   
                   
 -jtvFiles:{f1,f2,...,fn}
                   ['-jtvFiles:{f1,f2,...,fn}' to specify list of files
                    here rather than all in all of the files in the 
                    jtvInputDir. You can have multiple instances of this
                    switch.]
                    
 -jtvH:
                   ['-jtvHTMLgenerate' to generate a HTML file to invoke
                    the JTV applet for each JTV specification in the 
                    jtvInputDir. It puts the HTML file in the jtvOutputDir. 
                    Some of the non-JTV HTML modification switches are 
                    operable including: '-addEpilogue', '-addOutfilePostfix',
                    '-addProlog', '-mapQuestionmarks'. The default is to not
                    generate JTV HTML.]

 -jtvI:{input JTV directory}
                   ['-jtvInputDir:{input JTV directory}' to set the
                    input directory of JTV sub directories. This contains
                    the zipped or unzipped JTV files downloaded from mAdb.
                    Each zip file contains 3 files with (.atr,.cdt,.gtr) 
                    extensions. Default directory is 'JTVinput/'.]

 -jtvO:{output JTV directory}
                   ['-jtvOutputDir:{output JTV directory}' to set the
                    output directory of JTV sub directories. The converted
                    JTV directory and a corresponding HTML file are saved
                    there. Default directory is 'JTVoutput/'.]

 -jtvN:{mAdbArraySummary,mapHdrNamesFile,fromHdrName,toHdrName}
                   ['-jtvMapping:{mAdbArraySummaryFile,mapHdrNamesFile,
                    fromHdrName,toHdrName}' to convert a list of sub 
                    directories of JTV file sets by reading the three files
                    from the each of the subdirectories in the jtvInputDir
                    directory. The {mAdbArraySummaryFile} and {mapHdrNamesFile} 
                    are specified with a relative path. It maps the .cdt file
                    in each sub directory to use the {toHdrName} column of
                    the equivalent mapNamesFile map Table instead of 
                    the "EID:'mAdb ID'" as generated by mAdb. The mapping 
                    between "mAdb ID" and short array names is done using 
                    the {fromHdrName} column of the jtv_mAdbArraySummaryFile
                    Table map. It then writes out the JTV subset to a created
                    sub directory in jtvOutputDir that has the same base
                    name as the input JTV subdirectory being processed.
                    See the optional switches: '-jtvInputDir:{jtvInputDir}'
                    and '-jtvOutputDir:{jtvOutputSubDir}' to set the
                    directories to other than the defaults ("JTVinput" and
                    "JTVoutput"). The values for {fromHdrName} and {toHdrName}
                    should be in the of mapNamesFile.]

 -jtvR             [TODO]
                   ['-jtvReZipConvertedFiles' to reZip the converted files
                    in the output JTV directory in a file with the same name. 
                    Default is not to zip the converted files.]  
                    
                     
 -jtvTableDir:{tablesDirectory}'
                   ['-jtvTableDir:{tablesDirectory}' to set the various mapping
                    tables directory. These tables are used during various
                    conversion procedures. They include both the .txt and
                    the .map file (same file, but with different extensions).
                    Examples include: EGMAP.map(.txt), ExperimentGroups.map(.txt)
                    mAdbArraySummary.map(.txt). Note: this switch is used when
                    processing JTV files, but may also be set with the
                    '-tableDir:{tablesDirectory}' switch. The default directory
                    is 'data.Table/'.]

• Example 1 - no arguments.
• Example 2 - defaults arguements for Example 1.
• Example 3 - gets arguments from data/params.map file.
• Example 4 - converts set of simple EGxxx.txt Excel files.
• Example 4.1 - concatenates the set of similar EGxxx.txt Excel files to a single .txt file.
• Example 4.2 - extends Example 4.1 to generate a HTML file of a concatenated set of .txt files.
• Example 4.3 - extends Example 4.1 to generate a map file when creating a concatenated .txt file (the map could be used in the MRR conversions).
• Example 5 - converts an ExperimentGroup.txt Excel file.
• Example 5.1 - similar to Example 5 but exports large cells to small HTML files to make it more readable.
• Example 6 - converts a 2 sub-table spreadsheet (mAdb Retrieval Report). It also drops some columns, maps array names to 'GSP ID' names in EGxxx files, reorders colummns, sorts columns, and maps some bioinformatic DB keyword data to HREF links to those databases.
• Example 7 - similar to Example 6 but maps long names to 'Short GSP ID' names in EGxxx files.
• Example 8 - similar to Example 7, but specifies columns to keep rather than to drop.
• Example 9 - converts mAdb generated Java TreeView data by mapping array names, generating HTML JTV applet startup files.
• Example 10 - batch process a .doit file list of data.XXX/paramXXX.map conversions.
• Example 11 - edit a very large .txt file into another .txt file using the fast edit command.
• Example 12 - URL map multiple row header data in a transposed table.
• Example 13 - generate a Tests-Intersection .txt and .html table.
• Example 14 - generate a flipped tables with hyperlinked multi-line headers with data filtered by rows and column name filters.
• Example 15 - generate a set of batch jobs to convert data described in a table file generating summary Web pages, a set of params .map files in a tree structure.
• Example 16 - generates a .txt database file, an .idx Index Map file, and a .sidx Statistics Index Map file.
• Example 17 - the paramsSearchDefault.map file with additional information used by the search database GUI ("-searchGUI" option).

      HTMLtools data.GSPI-EG/params-GSPI-EG.map 
      
where: data.GSPI-EG/params-GSPI-EG.map 
contains:

 
#File:params-GSPI-EG.map
#"Revised: 3-30-2009"
#
-addPrologue:data.GSPI-ExpGrp/prolog.html
-addEpilogue:data.GSPI-ExpGrp/epilogue.html
-addRowNumbers
-addTableName:"GSP Experiment Group Samples"
-inputDir:data.GSPI-EG
-outputDir:html/GSP/GSP-Inventory/HTML
-tablesDir:data.Table
#
-extractRow:"Experiment Group ID (1),1,data.Table/ExperimentGroups.map,DL"
-alternateRowBackgroundColor:white
-shrinkBigCells:25,-5
-rmvTrailingBlankRowsAndColumns
#
#"----------- End --------- "

      HTMLtools data.GSPI-EG/params-GSPI-EG-concat.map 
      
where: data.GSPI-EG/params-GSPI-EG-concat.map 
contains:

#File:params-GSPI-EG-concatTXT.map
#"Revised: 3-29-2009"
#
-addPrologue:data.GSPI-EG/prolog.html
-addEpilogue:data.GSPI-EG/epilogue.html
-addRowNumbers
-addTableName:"GSP Inventory Concatenated List of all EG Samples"
-inputDir:data.GSPI-EG
-outputDir:data.Table
-tablesDir:data.Table
#
-alternateRowBackgroundColor:white
-shrinkBigCells:25,-5
-rmvTrailingBlankRowsAndColumns
#
#"Save the concatenated data in the following file."
#-concatTables:EGALLDataSet.txt
-concatTables:EGMAP.txt,noHTML
#
#"----------- End --------- "

      HTMLtools data.GSPI-EG/params-GSPI-EG-concatHTML.map 
      
where: data.GSPI-EG/params-GSPI-EG-concatHTML.map 
contains:

      HTMLtools data.Maps/params-Maps-EGMAP-map.map
       
where: data.Maps/params-Maps-EGMAP-map.map 
contains:

#File:params-Maps-EGMAP-map.map
#"Revised: 3-30-2009"
#"Generate the EGMAP.map file, but no HTML file."
#
-addRowNumbers
-addTableName:"Concatenation of all GSP Experiment Groups tables."
-inputDir:data.Table
-outputDir:data.Table
-tablesDir:data.Table
-files:"EGMAP.txt"
#
-alternateRowBackgroundColor:white
-shrinkBigCells:25,-5
-rmvTrailingBlankRowsAndColumns
#
-concatTables:EGMAP.map,noHTML
#
#"---------- end ---------"

      HTMLtools data.GSPI-ExpGrp/params-GSPI-ExpGrp.map
       
where: data.GSPI-ExpGrp/params-GSPI-ExpGrp.map 
contains:

#File:params-GSPI-ExpGrp.map
#"Revised: 3-30-2009"
#
-addPrologue:data.GSPI-ExpGrp/prolog.html
-addEpilogue:data.GSPI-ExpGrp/epilogue.html
-addRowNumbers
-addSubTitleFromInputFile
-addTableName:"GSP Experiment Groups Details"
-files:"ExperimentGroups.txt"
-inputDir:data.Table
-outputDir:html/GSP/GSP-Inventory/HTML
-tablesDir:data.Table
#
-alternateRowBackgroundColor:white
-shrinkBigCells:25,-5
-rmvTrailingBlankRowsAndColumns
#
-mapOptionsLists
-mapQuestionmarks:WHO,BOLD_RED
-mapQuestionmarks:WHAT,BOLD_RED
-mapQuestionmarks:WHEN,BOLD_RED
#
#"----------- End --------- "

      HTMLtools data.GSPI-ExpGrp/params-GSPI-ExpGrp-exportBigCells 
      
where: data.GSPI-ExpGrp/params-GSPI-ExpGrp-exportBigCells.map 
contains:

#File:params-GSPI-ExpGrp-exportBigCells.map
#"Revised: 3-30-2009"
#
-addOutfilePostfix:"-BRC"
-addPrologue:data.GSPI-ExpGrp/prolog.html
-addEpilogue:data.GSPI-ExpGrp/epilogue.html
-addRowNumbers
-addSubTitleFromInputFile
-addTableName:"GSP Experiment Groups Details"
-inputDir:data.Table
-outputDir:html/GSP/GSP-Inventory/HTML
-tablesDir:data.Table
-files:"ExperimentGroups.txt"
#
-alternateRowBackgroundColor:white
-shrinkBigCells:25,-5
-mapOptionsLists
-mapQuestionmarks:WHO,BOLD_RED
-mapQuestionmarks:WHAT,BOLD_RED
-mapQuestionmarks:WHEN,BOLD_RED
-rmvTrailingBlankRowsAndColumns
#
-exportBigCellsToHTMLfile:200
#
#"----------- End --------- "

      HTMLtools data.MRR/params-MRR.map
      
where: data.MRR/params-MRR.map  
contains:

      HTMLtools data.MRR/params-MRR-Short_GSP_ID.map
       
where: data.MRR/params-MRR-Short_GSP_ID.map  
contains:

#File:params-MRR-Short_GSP_ID.map
#"Revised: 5-28-2009"
#
-addOutfilePostfix:"-Short_GSP_ID"
-addPrologue:data.MRR/prolog.html
-addEpilogue:data.MRR/epilogue.html
-addRowNumbers
-addTableName:"mAdb Microarray Retrieval Report"
-inputDir:data.MRR
-outputDir:html/data.MRR
-outputDir:html
-tablesDir:data.Table
#
#"Limit the number of rows to the highest 500 fold-change values"
-limitMaxTableRows:"500,A-B Mean Difference,Descending"
#
-allowHdrDups
-alternateRowBackgroundColor:white
-rmvTrailingBlankRowsAndColumns
#-shrinkBigCells:25,-5
-shrinkBigCells:1,-5
-hdrLines:2
-hasEmptyLineBeforeTable
-makePrefaceHTML
-mapOptionsLists
#
#"Map header names. Select  from field='Affy .CEL file (16)'"
#"  to field= 'GSP ID (9)' or 'Simple GSP ID (10)'"
-mapHdrNames:"data.Table/EGMAP.map,Affy .CEL file (16),Simple GSP ID (10)"
#
#"Drop some of the columns"
-dropColumnColumn:"mgB36 Chr:Start-Stop"
-dropColumn:"mgB36 Cytoband"
-dropColumn:Annotation_Src
-dropColumn:UniGene
-dropColumn:RefSeq
-dropColumn:Refseqs_Hit
-dropColumn:geneIDS_Hit
-dropColumn:"Entrez GeneID"
-dropColumn:"Locus Tag"
-dropColumn:"BioCarta  Pathways"
-dropColumn:"KEGG Pathways"
#
#-dropColumn:"Gene Ontology Terms" (remove # if want to drop)
-dropColumn:"GO Tier2 Component"
-dropColumn:"GO Tier3 Component"
-dropColumn:"GO Tier2 Function"
-dropColumn:"GO Tier3 Function"
-dropColumn:"GO Tier2 Process"
-dropColumn:"GO Tier3 Process"
#"The following was added 5/28/09"
-dropColumn:"Map"
-dropColumn:"mgB37_Probe Chr:Start-Stop"
-dropColumn:"mgB37_Probe Cytoband"
-dropColumn:"mgB37_RefSeq Chr:Start-Stop"
-dropColumn:"mgB37_RefSeq Cytoband"
#
#"Reorder columns to left side of Table"
-reorderColumn:Gene,1
-reorderColumn:"A-B Mean Difference",2
-reorderColumn:Difference,3
-reorderColumn:"A Mean",4
-reorderColumn:"B Mean",5
-reorderColumn:"A-B p-Value",6
-reorderColumn:"p-Value",7
-reorderColumn:"Well ID",8
-reorderColumn:"Feature ID",9
-reorderColumn:"Description",10
#
#"Sort rows by column - use whichever comes first"
-sortRowsByColumn:"A-B Mean Difference",Descending
-sortRowsByColumn:Difference,Descending
-sortRowsByColumn:p-Value,Ascending
-sortRowsByColumn:Gene,Ascending
#
#"These map mAdb Feature Report data to Bioinformatics databases"
-hrefData:"Well ID",http://madb.nci.nih.gov/cgi-bin/clone_report.cgi?CLONE=WID%3A
-hrefData:Gene,http://www-bimas.cit.nih.gov/cgi-bin/cards/carddisp.pl?gene=
-hrefData:"Entrez GeneID",http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids=
-hrefData:"Feature ID",https://www.affymetrix.com/LinkServlet?probeset=
#
#"----------- End --------- "

      HTMLtools data.MRR/params-MRR-keep.map
       
where: data.MRR/params-MRR-keep.map
contains:

#File:params-MRR-keep.map
#"Revised: 4-9-2009"
#
-addOutfilePostfix:"-keep"
-addPrologue:data.MRR/prolog.html
-addEpilogue:data.MRR/epilogue.html
-addRowNumbers
-addTableName:"mAdb Microarray Retrieval Report"
-inputDir:data.MRR
-outputDir:html/data.MRR
-tablesDir:data.Table
#
-allowHdrDups
-alternateRowBackgroundColor:white
-rmvTrailingBlankRowsAndColumns
#-shrinkBigCells:25,-5
-shrinkBigCells:1,-5
-hdrLines:2
-hasEmptyLineBeforeTable
-makePrefaceHTML
-mapOptionsLists
#
#"Specify columns to keep, the rest are dropped"
-keepColumn:Gene 
-keepColumn:p-Value 
-keepColumn:Difference  
-keepColumn:"A-B p-Value"  
-keepColumn:"A-B Mean Difference" 
-keepColumn:"A Mean"  
-keepColumn:"B Mean"
-keepColumn:"Well ID" 
-keepColumn:"Feature ID" 
-keepColumn:Description 
-keepColumn:"Gene Ontology Terms"
#
#"Reorder columns to left side of Table"
-reorderColumn:Gene,1
-reorderColumn:"A-B Mean Difference",2
-reorderColumn:Difference,3
-reorderColumn:"A Mean",4
-reorderColumn:"B Mean",5
-reorderColumn:"A-B p-Value",6
-reorderColumn:"p-Value",7
-reorderColumn:"Well ID",8
-reorderColumn:"Feature ID",9
-reorderColumn:"Description",10
#
#"Sort rows by column - use whichever comes first"
-sortRowsByColumn:"A-B Mean Difference",Descending
-sortRowsByColumn:Difference,Descending
-sortRowsByColumn:p-Value,Ascending
-sortRowsByColumn:Gene,Ascending
#
#"These map mAdb Feature Report data to Bioinformatics databases"
-hrefData:"Well ID",http://madb.nci.nih.gov/cgi-bin/clone_report.cgi?CLONE=WID%3A
-hrefData:Gene,http://www-bimas.cit.nih.gov/cgi-bin/cards/carddisp.pl?gene=
-hrefData:"Entrez GeneID",http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=graphics&list_uids=
-hrefData:"Feature ID",https://www.affymetrix.com/LinkServlet?probeset=
#
#"----------- End --------- "

      HTMLtools JTVinput/params-JTV.map
      
where: params-JTV.map  
contains:

       HTMLtools -batchProcess:batchList.doit
       
where: batchList.doit
contains:

      HTMLtools data.MRR-all/params-MRR-all-fast.map 
      
where: data.MRR-all/params-MRR-all-fast.map  
contains:

      HTMLtools data.MRR-GL-examples/params-MRR-GL-GeneList.map 
      
where: data.MRR-GL-examples/params-MRR-GL-GeneList.map  
contains:

      HTMLtools data.TestsIntersection/params-TestsIntersection-ALL.map 
      
where: data.TestsIntersection/params-TestsIntersection-ALL.map  
contains:

#File:params-TestsIntersection-ALL.map
#"Revised 5-06-2009"
#
#"[1] Master script to create a Tests Intersection Table file for all tests"
#"in the mAdb-TestsToDo.txt file that we have data."
#
-inputDir:data.GBS
-outputDir:html/GSP/TestsIntersection
#
#"Limit the number of rows to the highest 500 fold-change values"
-limitMaxTableRows:"500,Range FC,Descending"
#
#"The tablesDir subdir. where mapping and other reference Tables are copied"
#"to the batchScripts directory."
-tablesDir:data.Table
#
-allowHdrDups
-rmvTrailingBlankRowsAndColumns
-hdrLines:2
-hasEmptyLineBeforeTable
#
-makeTestsIntersectionTable:"mAdb-TestsToDo.txt"
#
#"Add FC range computations and expand the TI table with"
#"fields ('Max FC', 'Min FC', 'Range FC')."
-addFCrangesForTestsIntersectionTable
#
#"Add the ('Range A Mean', 'Range B Mean', 'FC counts %') computations to"
#"an expanded TestsIntersectionTable table."
-addRangeOfMeansToTItable 
#
#"Save the edited table as a .txt file"
-saveEditedTable2File:"TestsIntersection-ALL.txt,HTML"
-mapDollarsigns:$$EXCEL-FILE$$,"TestsIntersection-ALL.txt"
#
#"The mAdb-TestsToDo.txt Tables are in"
#"the '-tablesDir:data.Table' subdirectory."
#
#"[2] Now after the Tests-Intersection .txt table is saved, generate the HTML file."
#"Note: Converter removes -hasEmptyLineBeforeTable and sets -hdrLines:5 switches."
#
-addPrologue:data.TestsIntersection/prolog-TI.html
-addEpilogue:data.TestsIntersection/epilogue-TI.html
#
#
-addRowNumbers
-addTableName:"Intersection of All GSP Fold-Change Tests for Genes in any test"
-mapDollarsigns:$$TITLE$$,"All GSP Tests for Genes in any test"
-allowHdrDups
#
-alternateRowBackgroundColor:white
#-shrinkBigCells:25,-5
-shrinkBigCells:1,-5
#
###-sortRowsByColumn:Gene,Ascending
-sortRowsByColumn:"Range FC",Descending
#
#"These map mAdb Feature Report data to Bioinformatics databases"
-hrefData:"Well ID,http://madb.nci.nih.gov/cgi-bin/clone_report.cgi?CLONE=WID%3A"
-hrefData:"Gene,http://www-bimas.cit.nih.gov/cgi-bin/cards/carddisp.pl?gene="
-hrefData:"Feature ID,https://www.affymetrix.com/LinkServlet?probeset="
#
#"------------- End ---------------"

Example 14.1

      HTMLtools data.flip/params-MRR-all-fastSave+MakeIndex.map 
      
where: data.flip/params-MRR-all-fastSave+MakeIndex.map  
contains:

#File:params-MRR-all-fastSave+MakeIndex.map
#"This saves the edited Table and then makes an Index-Map file"
#"of the saved edited table."
#"Revised 6-23-2009"
#
-inputDir:data.MRR-all
-outputDir:data.MRR-flip
-tablesDir:data.Table
#
-files:"Review-LH-18Arrays-54-pathway-Genes-in-JakStat.txt"
#
#"Save the edited table as a .txt file"
-saveEditedTable2File:EGALLDataSet.txt,noHTML
#
#"Make an EGALLDataSet.idx index file of the .txt file"
-makeIndexMapFile:"Gene,Well ID,Feature ID"
#
-allowHdrDups
-rmvTrailingBlankRowsAndColumns
-hdrLines:2
-useOnlyLastHeaderLine
-hasEmptyLineBeforeTable
#
#"Do a fast edit of the .txt file"
-fastEditFile
-noHTML
#
#"Map header names. Select  from field='Affy .CEL file (16)'"
#"  to field= 'GSP ID (9)' or 'Simple GSP ID (10)'" 
-mapHdrNames:"data.Table/EGMAP.map,Affy .CEL file (16),GSP ID (9)"
#
#"Drop more columns for simplest file"
-dropColumn:Difference
-dropColumn:p-Value
-dropColumn:Description
#"Drop some of the columns"
-dropColumnColumn:"mgB36 Chr:Start-Stop"
-dropColumn:"mgB36 Cytoband"
-dropColumn:Annotation_Src
-dropColumn:UniGene
-dropColumn:RefSeq
-dropColumn:Refseqs_Hit
-dropColumn:geneIDS_Hit
-dropColumn:"Entrez GeneID"
-dropColumn:"Locus Tag"
-dropColumn:"BioCarta  Pathways"
-dropColumn:"KEGG Pathways"
-dropColumn:"Gene Ontology Terms" (remove # if want to drop)
-dropColumn:"GO Tier2 Component"
-dropColumn:"GO Tier3 Component"
-dropColumn:"GO Tier2 Function"
-dropColumn:"GO Tier3 Function"
-dropColumn:"GO Tier2 Process"
-dropColumn:"GO Tier3 Process"
#"The following was added 5/28/09"
-dropColumn:"Map"
-dropColumn:"mgB37_Probe Chr:Start-Stop"
-dropColumn:"mgB37_Probe Cytoband"
-dropColumn:"mgB37_RefSeq Chr:Start-Stop"
-dropColumn:"mgB37_RefSeq Cytoband"
#
#"Sort the rest of the columns alphabetically"
-reorderRemainingColumnsAlphabeticly
#
#"Reorder columns to left side of Table"
-reorderColumn:Gene,1
-reorderColumn:"A-B Mean Difference",2
-reorderColumn:Difference,3
-reorderColumn:"A Mean",4
-reorderColumn:"B Mean",5
-reorderColumn:"A-B p-Value",6
-reorderColumn:"p-Value",7
-reorderColumn:"Well ID",8
-reorderColumn:"Feature ID",9
-reorderColumn:"Description",10
#
#"----------- End ----------- "

      HTMLtools data.flip/params-MRR-flipGID-all-GeneListNames+FeatureIDnames-RowNames.map 
      
where: data.flip/params-MRR-flipGID-all-GeneListNames+FeatureIDnames-RowNames.map

#File:params-MRR-flipGID-all-GeneListNames+FeatureIDnames-RowNames.map
#"Revised 7-18-2009"
#
-addPrologue:data.MRR-flip/prolog.html
-addEpilogue:data.MRR-flip/epilogue.html
-addRowNumbers
-addTableName:"Flipped 18 GSP Mouse MOE403_2 arrays Filtered by Feature_ID List"
#
-inputDir:data.MRR-flip
-outputDir:html/data.flip
-tablesDir:data.Table
#
-addOutfilePostfix:"-GeneList+FeatureID-RowNames"
#
-flipTableByIndexMap:"EGALLDataSet.txt,EGALLDataSet.idx"
-flipColumnName:"*LIST*,Gene,Socs1,Socs2,Socs3,Stat1,Stat2,Stat3,Stat4,Stat5a,Stat5b"
-flipColumnName:"*LIST*,Well ID,"
-flipColumnName:"*LIST*,Feature ID,1418507_s_at,1449109_at, 1438470_at,1441476_at"
-flipRowNames:"*LIST*,EG001,EG003.1,EG003.2"
-flipOrder:"Gene,Well ID,Feature ID"
#
-allowHdrDups
-alternateRowBackgroundColor:white
-rmvTrailingBlankRowsAndColumns
#
#-shrinkBigCells:25,-5
-shrinkBigCells:1,-5
#
#"This does multiple header-row data mapping."
-hrefHeaderRowMapping
#
#"These map mAdb Feature Report data to Bioinformatics databases"
-hrefData:"Well ID",http://madb.nci.nih.gov/cgi-bin/clone_report.cgi?CLONE=WID%3A
-hrefData:Gene,http://www-bimas.cit.nih.gov/cgi-bin/cards/carddisp.pl?gene=
-hrefData:"Feature ID",https://www.affymetrix.com/LinkServlet?probeset=
#
#"--------- End ---------"

      HTMLtools data.GBS/params-genBatchScripts.map 
      
where: data.GBS/params-genBatchScripts.map  
contains:

#File:params-genBatchScripts.map
#"Revised 4-26-2009"
#
#"Master script to generate params .map files and buildWebPages.doit"
#"file for all tests in the mAdb-TestsToDo.txt file. It generates an"
#"environment in batchScripts/ to enable running all of the scripts as"
#"a Window's batch job buildWebPages.bat on the buildWebPages.doit batch"
#"input list Windows batch startup file."
#
#"The templates (.html, .param) and .map files are in the same directory"
#"as this master batch generation script."
#
#"Map: mAdb-TestsToDo.txt - test Table to drive the batch scripts generation."
#
#"Map: CellTypeTissue.map - maps 'Introduction' field for 'Tissues'."
#"Map: ExperimentGroups.map - maps 'Details' field for 'Expression Groups'."
#"Map: EGMAP.map - maps 'Affy .CEL file' name to 'Simple GSP ID' or 'GSP ID'."
#
#"Arg: batchScripts - where all files and the following subdirectories are saved"
#"Arg: ParamScripts - subdir. where generated params*.map files are copied"
#"Arg: inputTree - subdir. where mAdb generated .txt MRR and JTV data are copied"
#"Arg: Summary - subdir. where generated text HTML top level Web pages are saved"
#"Arg: Analyses - subdir. where generated text HTML & edited .txt files are saved"
#"Arg: JTV - subdir. where generated JTVtext HTML & edited JTV files are saved"
#"Arg: JTVjars - subdir. where the JTV runtime jar files are copied"
#
-inputDir:data.GBS
-outputDir:batchScripts
#
#"The tablesDir subdir. where mapping and other reference Tables are copied"
#"to the batchScripts directory."
-tablesDir:data.Table
#
-genBatchScripts:"batchScripts,ParamScripts,InputTree,Summary,Analyses,JTV"
-rmvTrailingBlankRowsAndColumns
#
#"The following maps and Tables are in the '-tablesDir:data.Table' subdirectory."
-genMapHdrNames:"EGMAP.map"
-genMapEGdetails:"ExperimentGroups.map"
-genMapIntroduction:"CellTypeTissue.map"
-genTestFiles:"mAdb-TestsToDo.txt"
#
#"Create Tests-Intersection (TI) HTML links in summary file & params .map files."
-genTestsIntersection
#
#"List of CellType/Tissue summary templates for generating the Summary pages"
-genSummaryTemplate:1,summaryTemplateProlog.html
-genSummaryTemplate:2,summaryTemplateExperimental.html
-genSummaryTemplate:3,summaryTemplateAnalysis.html
-genSummaryTemplate:4,summaryTemplateFurtherAnalysis.html
-genSummaryTemplate:5,summaryTemplateEpilogue.html
#
#"List of params .map templates for generating batch params .map files."
-genParamTemplate:MRR,paramsTemplate-MRR.map
-genParamTemplate:MRR-keep,paramsTemplate-MRR-keep.map
###-genParamTemplate:JTV,paramsTemplate-JTV.map
-genParamTemplate:JTV,paramsTemplate-JTV-jtvReZip.map
-genParamTemplate:MRR-saveFile,paramsTemplate-MRR-saveFile.map
-genParamTemplate:TI,paramsTemplate-TI.map
#
#"List of support files to be copied to support -batchProcess of the .doit file."
-genCopySupportFile:"../HTMLtools.jar"
-genCopySupportFile:"../ReferenceManual.html"
-genCopySupportFile:prologMRR.html
-genCopySupportFile:prologJTV.html
-genCopySupportFile:prologTI.html
-genCopySupportFile:epilogueMRR.html
-genCopySupportFile:epilogueJTV.html
-genCopySupportFile:epilogueTI.html
#
#"List of JTV support files to be copied to support -batchProcess of the .doit file."
#-genCopySupportFile:JTVjars/TreeViewApplet.jar
#-genCopySupportFile:JTVjars/nanoxml-2.2.2.jar
#-genCopySupportFile:JTVjars/plugins/Dendrogram.jar
#-genCopySupportFile:JTVjars/plugins/Karyoscope.jar
#-genCopySupportFile:JTVjars/plugins/Scatterplot.jar
#-genCopySupportFile:JTVjars/plugins/Treeanno.jar
#
#"Copy tree data to top level batch scripts subdirectory"
-genTreeCopy:JTVjars,batchScripts/JTVjars

#"Copy Mapping files tree data to top level batch scripts subdirectory"
-genTreeCopy:data.Table,batchScripts/data.Table
#
#"Copy input data tree data to batch scripts subdirectory"
-genTreeCopy:data.GBS/CellTissue,batchScripts/inputTree/CellTissue
#
#"------------- End ---------------"

      HTMLtools data.MRR-all/params-MRR-all-fastSave.map 
      
where: data.MRR-all/params-MRR-all-fastSave.map  
contains:

#File:params-MRR-all-fastSave.map
#"Revised 8-18-2009"
#"Convert MRR all arrays file to edited DB 'EGALLDataSet.txt' file."
#
-inputDir:data.MRR-all
-outputDir:data.MRR-all
-tableDir:data.Table
#
-files:"EG1+EG3.1+EG3.2-MSE430_2-18Arrays-RMA-Grouped.txt"
#
#
#"Save the edited table as a .txt file"
-saveEditedTable2File:EGALLDataSet.txt,noHTML
#
#"Do a fast edit of the .txt file and don't generate HTML file"
-fastEditFile
#-noHTML
#
#-addOutfilePostfix:"-edit"
#
-allowHdrDups
-rmvTrailingBlankRowsAndColumns
-hdrLines:2
-useOnlyLastHeaderLine
-hasEmptyLineBeforeTable
#
#"Map header names. Select  from field='Affy .CEL file (16)'"
#"  to field= 'GSP ID (9)' or 'Simple GSP ID (10)'" 
-mapHdrNames:"data.Table/EGMAP.map,Affy .CEL file (16),GSP ID (9)"
#
#"Drop more columns for simplest file"
-dropColumn:Difference
-dropColumn:p-Value
-dropColumn:Description
#"Drop some of the columns"
-dropColumnColumn:"mgB36 Chr:Start-Stop"
-dropColumn:"mgB36 Cytoband"
-dropColumn:Annotation_Src
-dropColumn:UniGene
-dropColumn:RefSeq
-dropColumn:Refseqs_Hit
-dropColumn:geneIDS_Hit
-dropColumn:"Entrez GeneID"
-dropColumn:"Locus Tag"
-dropColumn:"BioCarta  Pathways"
-dropColumn:"KEGG Pathways"
-dropColumn:"Gene Ontology Terms" (remove # if want to drop)
-dropColumn:"GO Tier2 Component"
-dropColumn:"GO Tier3 Component"
-dropColumn:"GO Tier2 Function"
-dropColumn:"GO Tier3 Function"
-dropColumn:"GO Tier2 Process"
-dropColumn:"GO Tier3 Process"
#"The following was added 5/28/09"
-dropColumn:"Map"
-dropColumn:"mgB37_Probe Chr:Start-Stop"
-dropColumn:"mgB37_Probe Cytoband"
-dropColumn:"mgB37_RefSeq Chr:Start-Stop"
-dropColumn:"mgB37_RefSeq Cytoband"
#
#"Sort the remaining columns alphabetically"
-reorderRemainingColumnsAlphabeticly
#
#"Reorder columns to left side of Table"
-reorderColumn:Gene,1
-reorderColumn:"A-B Mean Difference",2
-reorderColumn:Difference,3
-reorderColumn:"A Mean",4
-reorderColumn:"B Mean",5
-reorderColumn:"A-B p-Value",6
-reorderColumn:"p-Value",7
-reorderColumn:"Well ID",8
-reorderColumn:"Feature ID",9
-reorderColumn:"Description",10
#
#"----------- End --------- "

Example 16.2 - generates an .idx Index Map file of the database file

      HTMLtools data.MRR-all/params-MRR-all-fastMakeIndex.map 
      
where: data.MRR-all/params-MRR-all-fastMakeIndex.map  
contains:

#File:params-MRR-all-fastMakeIndex.map
#"Revised: 8-19-2009"
#
-inputDir:data.MRR-all
-outputDir:data.MRR-all
-tablesDir:data.Table
#
-files:"EGALLDataSet.txt"
#
-hdrLines:1
#
#"Do a fast edit of the .txt file"
-fastEditFile
#
#"Make an .idx index file of the .txt file"
-makeIndexMapFile:"Gene,Well ID,Feature ID"
#
#"----------- end --------- "

Example 16.3 - generates a .sidx global StatisticsIndex Map file of the database file

      HTMLtools data.MRR-all/params-MRR-all-fastMakeStatisticsIndex.map 
      
where: data.MRR-all/params-MRR-all-fastMakeStatisticsIndex.map  
contains:

#File:params-MRR-all-fastMakeStatisticsIndex.map
#"Revised: 8-11-2009"
#
-inputDir:data.MRR-all
-outputDir:data.MRR-all
-tablesDir:data.Table
#
#"Specify the edited data set file to use. It is assumed that"
#"the IndexMap file was created and has a .idx file extension."
-files:"EGALLDataSet.txt"
#
-hdrLines:1
#
#"Specify columns to drop when analyzing the Statistics, the rest are dropped."
-dropColumn:Gene
-dropColumn:"Well ID" 
-dropColumn:"Feature ID" 
#
#"Make an .sidx index file of the .txt and .idx files"
-makeStatisticsIndexMapFile
#
#"----------- end --------- "

Example 17 - the paramsSearchDefault.map file used with the "-searchGui" option

      HTMLtools -searchGui 
      
where: this looks for the file data.search/paramsSearchDefault.map  
contains:

#File:paramsSearchFlip.map
#"$$DATE$$"
#
#"Search information read by the search GUI for prompts and menus"
-searchTermNames:"Gene,Well ID,Feature ID"
-searchRowFilterName:"Sample Experiment Groups"
-searchSampleChoiceFile:sampleExperimentGroupsChoices.txt
-searchTermsDemoData:"Stat5a Stat5b 1438470_at 1441476_at 1446085_at"
-searchUserTermList:"LitRefGeneList.txt,Feature ID,Literature Review"
-searchTermsFilterPrompt:"'Gene', 'Well ID', and/or 'Probe' names. E.g., Stat5a, Stat5b, 1438470_at 1441476_at 1446085_at, etc."
-searchRowFilterPrompt:"'Sample Experiment Groups'. E.g., select one or more Experiment Groups"
#
-addPrologue:data.search/prolog.html
-addEpilogue:data.search/epilogue.html
-addTableName:"$$DATA_SOURCE_SUBTITLE$$"
-addRowNumbers
#
-addTableName:"Search database filtered by Gene and/or Probe IDs and Experiment Groups"
#
-inputDir:data.search
-outputDir:data.search
-tablesDir:data.Table
#
-addOutfilePostfix:"-search"
#
#"Database (.txt) and index map of database (.idx) to search" 
-flipTableByIndexMap:"EGALLDataSet.txt,EGALLDataSet.idx"
#
$$SEARCH_FILTERS$$
#
#"Maps to:"
# '-flipOrder:"Gene,Well ID,Feature ID"'
# '-flipColumnName:"*LIST*,Gene,g1,g2,...gn"'
# '-flipColumnName:"*LIST*,Well ID,w1,w2,...,wk"'
# '-flipColumnName:"*LIST*,Feature ID,f1,f2,...,fm"'
# '-flipRowNames:"*LIST*,s1,s2,...,sp"'
# '-dataPrecisionHTMLtable:-1'
# '-showDataHeatmapFlipTable'
# '-flipUseExactColumnNameMatch:TRUE'
#
-allowHdrDups
-alternateRowBackgroundColor:white
-rmvTrailingBlankRowsAndColumns
#
#-shrinkBigCells:25,-5
-shrinkBigCells:1,-5
#
#"This does multiple header-row data mapping."
-hrefHeaderRowMapping
#
#"These map mAdb Feature Report data to Bioinformatics databases"
-hrefData:"Well ID",http://madb.nci.nih.gov/cgi-bin/clone_report.cgi?CLONE=WID%3A
-hrefData:Gene,http://www-bimas.cit.nih.gov/cgi-bin/cards/carddisp.pl?gene=
-hrefData:"Feature ID",https://www.affymetrix.com/LinkServlet?probeset=
#
#"--------- End ---------" 

1. data.GSPI-EG/ contains the EG001.txt through EGxxx.txt (or more as new experiment groups are added) files (saved as tab-delimited .txt from the Excel GSP-Inventory.xls spreadsheets). It also includes the EGMAP.txt concatenated file (generated by HTMLtools using the -concatTables command), and prolog.html and epilogue.html template files configured for EG data. There are three script files for mapping the data: params-EG.map for mapping all of the EGxxx.txt files; params-EG-concatTXT.map for generating the EGMAP.txt file (in the data.Table// directory). The params-EG-concatTXT.map generates the EGMAP.html file. The data.Maps/params-Maps-EGMAP-map.map generates the data.Table/EGMAP.map file used for mapping sample names to a short consistent names in may of the other scripts. The data.Maps/ also contains a script to create the ExperimentGroups.map file (from the ExperimentGroups.txt) for extracting experiment specific information for the corresponding EGxxx row to include in the epilogue for the EGxxx.html files. Similarly for the mAdbArraySummary.map file (used with the JTV conversions and was export as a mAdb Array Summary). The generated HTML files are saved in the html/GSP/GSP-Inventory/ directory.

2. data.GSPI-ExpGrp/ contains the ExperimentGroups.txt file (saved as tab-delimited .txt from Excel spreadsheet), and prolog.html and epilogue.html files configured for ExperimentGroups data. The script file params-GSPI-ExpGrp.map specifies how to convert the .txt file). The generated HTML files are saved in the html/GSP/GSP-Inventory/ directory.

3. data.MRR/ contains the some examples of mAdb Retrieval Reports (MRR) with .txt file extensions for generating various types of HTML web pages. It uses a several mapping files generated in data.Maps/ in doing the MRR HTML Web page generation. The prolog.html and epilogue.html files are configured for MRR type data. There are several params-MRR*.map script files. As the MRR input data files each contains two tables, the -makePrefaceHTML will generate additional "preface-" HTML files linked from the generated HTML files. The generated HTML files are saved in the html/data.MRR directory. Note that this is a demonstration directory, not used for the GSP Web site, to illustrate the various HTML conversion options. The actual data for the GSP database is generated in the GenBatchScripts Example 13.

4. Another demonstration data set is in JTVinput/ that contains some sample Java TreeView data sets, a prolog.html and epilogue.html configured for JTV data (see Example 9). It uses the data.Table/mAdbArraySummary.map and data.Table/EGMAP.map map files for mapping the mAdb unzipped JTV mAdb ID array names to GSP ID names. The params-JTV.map specifies how to map the data. The JTVjars/ contains the set of Java Tree View .jar files required to run the generated HTML files. The '-jtvCopyJTVjars' switch (in the script) will copy the required .jar files to the output directory. The converted JTV files, generated HTML files (along with the copied JTV .jar files) are saved in the html/JTVoutput/ directory. Note that this is a demonstration directory, not used for the GSP Web site, to illustrate the various conversion options. The actual data for the GSP database is generated in the GenBatchScripts Example 13.

5. data.Table/ contains the tab-delimited .txt files for the mapping tables as well as the .map files by running the scripts in the data.Maps/ directory.

6. data.TestsIntersection/ contains the scripts for creating a Tests-Intersection .txt and .html file shown in the html/GSP/TestsIntersection/ directory (see Example 13) .

7. data.all/ contains data and scripts for using the -fastEditFile option to handle very large input files. The edited .txt files are saved in data.all/.

8. data.flip/ contains data and scripts for using the -fastEditFile option to handle very large input files. The edited .txt files are saved in data.flip/ and the .html file shown in the html/data.flip/ directory (see Example 14).

9. data.search/ contains data and scripts for using the -searchGui option to to use with the Search Database GUI. The database files and results files are saved in data.search/ directory (see 2.1.2 Search Database GUI).

10. data.GBS/ contains the params-genBatchScripts.map script (see Example 15) and support data for generating batch scripts (for subsequent processing). The set of tests to generate the params .map files is described in data.Table/mAdb-TestsToDo.txt that in turn was saved as a tab-delimited file from the Excel spreadsheet mAdb-TestsToDo.xls. It uses mapping files EGMAP.map, ExperimentGroups.map, CellTypeTissue.map in data.Maps/ as well as various templates in data.GBS/ for params .map, summary HTML templates, and prolog and epilogue HTML templates used when execcuting the batch scripts. The generated batch scripts and support data is saved in a created directory batchScripts/. The generated parameter .map scripts are saved in the batchScripts/ParamScripts/ directory. The generated Tissue summary HTML Web pages are saved in the batchScripts/Summary/ directory. The input data required when running the generated batch scripts are copied to the batchScripts/inputTree directory. The generated test data HTML web pages generated when the generated batch scripts are run will be saved in the batchScripts/Analyses/ directory. The generated JTV test data HTML web pages and edited JTV data when the generated batch scripts are run will be saved in the batchScripts/JTV/ directory. Additional files generated are the batchScripts/buildWebPages.doit params .map scripts to execute and the Windows .BAT file batchScripts/buildWebPages.bat to start the batch processing.

  
java -Xmx256M -classpath .;.\HTMLtools.jar HTMLtools \
          -genBatchScripts:data.GBS/params-genBatchScripts.map

The program was built using Eclipse (Version 3.4) (www.eclipse.org). The distibution includes the ANT (ant.apache.org) build.xml script that could be used either standalone or with some Integrated Development Environment such as Eclipse (which includes ANT). There is a separate javadocs .BAT file javadocs-HTMLtools.bat that can be used for generated the java class documentation in the javadocs/ directory. The .BAT files are renamed in the initial .zip file distribution and need to be unpacked before use (see Section 2.1 for details).

• HTMLtools.java - main class and contains the top-level process loop. It extends class Globals.
• Globals.java - contains the global variables.
• ConvertGUI.java - converter graphical user interface (GUI)
• ProcessData.java - thread to process CvtGUI data
• Convert.java - contains the Table-to-HTML converters and various mapping methods.
• DataRowStatisticsIndexMap.java - computes the global Statistics Index Map when generate .sidx file.
• JTVconvert.java - JTV array-name mapping and HTML generation methods.
• FileIO.java - methods for file I/O and zip file I/O.
• FileTable.java - Table readers and manipulation methods.
• GenBatchScripts.java - generate batch scripts from methods.
• MakeFlipTable.java - create a flipped Table methods.
• MakeTestsIntersectionTbl.java - create a Tests-Intersection Table.
• SearchGUI.java - specialized database search GUI
• ProcessLoadIndexMapData.java - thread to load .idx or .sidx in the background for SearchGUI
• ProcessDataSearch.java - thread to process SearchGUI data
• Sort.java - sort methods used in sorting Table rows.
• Switches.java - the command line switch parser.
• UtilCM.java - various short utility methods.
• TODO.java - list of additional options under development.

The user enters search information into the SearchGui interface to specify 1. a list of genes and/or Well IDs and/or Feature IDs (gene probe IDs); and then, 2. select one or more experiment groups. When they press the Process button, it creates a custom script data.search/paramSearchFlip.map from a default data.search/paramsSearchDefault.map script that is domain dependent. Then it creates a new thread (ProcessDataSearch.java) and recursively calls HTMLtools to execute the just generated paramSearchFlip.map script file. The script includes the flip table options to actually generate the flipped table on the specified subset of data. When the thread is done processing, it has generated data.search/EGALLDataSet-search.txt and data.search/EGALLDataSet-search.html files. It then lets the user press the View HTML button to pop up a web brower to see the EGALLDataSet-search.html file. In the example data.search/paramSearchFlip.map, it has flip options specified from a merging of the user-specified data along with other data (see the file for the rest of the default options)

   . . .
#"Database (.txt) and index map of database (.idx) to search"
-flipTableByIndexMap:"EGALLDataSet.txt,EGALLDataSet.idx"
#
-flipOrderHdrColNames:"Gene,Well ID,Feature ID"
-flipColumnName:"*LIST*,Gene,Stat5a,Stat5b"
-flipColumnName:"*LIST*,Feature ID,1438470_at,1441476_at,1446085_at"
-flipRowFilterNames:"*LIST*,EG002,EG003.1,EG003.2"
#
#"Set the data precision for generated HTML."
-dataPrecisionHTMLtable:0
#
#
#"Set the flip-table sort by column name."
-sortFlipTableByColumnName:"Stat5b"
#
#"Generate heat-map data cells in a HTML conversion if .sidx exists."
-showDataHeatmapFlipTable
#
    . . .

Flip table computation

The flip table option uses three precomputed database files (created with HTMLtools): data.search/EGALLDataSet{.txt,.idx,.sidx} that allow us to random access any row by probe ID. (A gene may have 1 to half a dozen probe IDs). Since the number of genes that would be used in a search is relatively small (under 100 - typically a lot less on the order of 10 to 20), gathering the data is relatively fast. The script file specifies -flipTableByIndexMap:"EGALLDataSet.txt,EGALLDataSet.idx".

If the heatmap option is used, then it uses the EGALLDataSet.sidx file instead (i.e., Statistics Index Map file). This contains the same row seek data as the .idx file, but also statistics (min, max, mean, stddev) for each row and for the entire database. This is then used to map each table data cell value to a cell background color to implement the heat map.

In addition to the heatmap option (default), it also lets you adjust the precision of the data (which normally has 3 or 4 digits) to 0 or more digits, and to sort the rows by the data in a particular gene/probe ID column.

So the processing is broken into two parts: the GUI part (SearchGui) to gather the arg list to generate the paramSearchFlip.map file, and the flip table generate part to build the search results heatmap HTML table.

This section documents the batchScripts/ directory for creating Web pages and briefly describes the 1) contents of the batchScripts/ directory, 2) how it is created using the GenBatchScripts (GBS) facility of this converter program using the list of mAdb tests and data from those tests, and 3) finally how it is used to create Web pages suitable for copying to the Jak-Stat Prospector (J-S P) Web server on http://jak-stat.nih.gov/. This example could serve as a model for developing static Web server pages for other types of analysis system generated data to be used on a static Web server.

Before attempting to run the GenBatchScripts process to create the batchScripts/ directory, we recommend you familiarize your self with the commands in this Reference Manual. The batchScripts/ directory contains a Windows .bat file to run the HTMLtools program, buildWebPages.bat, and a list of conversion batch jobs in buildWebPages.doit. The buildWebPages.doit file contains a list of generated conversions to be performed in converter-batch (as opposed to Windows-batch). Each conversion is in the form of a generated parameter .map file saved in the batchScripts/ParamsScripts/ directory. (In the rest of this discussion for brevity, we will omit the batchScripts/ prefix in mentioning these directories where it is unambiguous.)

There are additional support files that are required for updating the J-S P Web server tree. These are described at the end of this document in the discussion on converting data from GSP-Inventory for the J-S P.

7.1 Overview of Conversion Process

 
  ParamScripts/      - GBS generated conversion params*.map files
  InputTree/         - mAdb generated .txt MRR and JTV data are copied by GBS
  Summary/           - GBS generated text HTML top level Web pages
  Analyses/          - GBS generated text HTML & edited .txt files
  JTV/               - GBS generated JTVtext HTML & edited JTV files 
  JTVjars/           - the JTV runtime jar files are copied by GBS
  data.Table/        - the common mapping files are copied by GBS
  buildWebPages.doit - GBS generated -batch script to convert MRR and JTV data
  buildWebPages.bat  - GBS generated Windows BAT file run converter on .doit file

  ExperimentGroups.map     - Experiment Group info by EGxxxx
  CellTypeTissue.map       - Tissue 'Introduction' by EGxxxx for summaries
  EGMAP.map                - map 'Affy .CEL file' names to 'GSP ID's
  mAdbArraySummary.map     - the 'mAdb ID' by 'Affy .CEL file'

  summaryTemplateProlog.html
  summaryTemplateExperimental.html
  summaryTemplateAnalysis.html
  summaryTemplateFurtherAnalysis.html
  summaryTemplateEpilogue.html

Mapping $$keywords$$ used with the HTML SummaryTemplate files

  $$TISSUE$$            - tissue associated with the test
  $$INTRODUCTION$$      - Introduction data from the CellTypeTissue.map file
  $$LIST_EXPR_GROUPS$$  - list of expression groups used in the test
  $$DESCRIPTION$$       - description using data from mAdb-TestsToDo data
  $$ANALYSIS$$          - data generated for the "Further Analysis" section
  $$FUTHERANALYSIS$$    - data generated for the "Further Analysis" section
  $$DATE$$              - date of conversion
  $$INFILENAME$$        - specific test name (e.g., EG1-test-1+FC-ALL.txt)  

  paramsTemplate-MRR.map          - generate MRR gene expression HTML report
  paramsTemplate-MRR-keep.map     - generate MRR gene list HTML report
  paramsTemplate-JTV-jtvReZip.map - generate mapped JTV data and JTV HTML applet

  $$DATE$$              - date of conversion
  $$INPUT_DATA$$        - input data relative directory 
  $$OUTPUT_DATA$$       - output data relative directory
  $$TABLE_DATA$$        - location of the .map files relative directory
  $$A_SAMPLE_NAME$$     - name of the 'A' condition
  $$B_SAMPLE_NAME$$     - name of the 'B' condition
  $$$$JTV_JARS$$$$      - location of the JTV runtime .jar support files directory
    
  $$TISSUE.2$$          - tissue associated with the test 
  $$PAGE_LABEL.2$$      - data from page label in mAdb-TestsToDo for test entry
  $$DESCRIPTION.2$$     - data from description in mAdb-TestsToDo for test entry
  $$CLASS_A.2$$         - list of GSP IDs for condition A
  $$CLASS_B.2$$         - list of GSP IDs for condition B  

  $$PROLOG$$            - name of prolog file prologMRR.html or prologJTV.html
  $$EPILOGUE$$          - name of prolog file epilogueMRR.html or epilogueJTV.html
  $$TITLE.2$$           - title for specific generated Web page 
  $$TEST_OR_ALL.2$$     - "Test" or "All" modifierp     
  $$GBS_DESCRIPTION.2$$ - test specific information        
  $$PARAM_MAP_NAME$$    - name of parameter file with (+-FC, -ALL, -JTV) modifiers         
  $$TESTMAME.2$$        - test name with (+-FC, -ALL, -JTV) modifiers       
  $$FILE.2$$            - data input file for each params .map       
  $$JOIN_TABLE_FILE.2$$ - the -joinTableFile file for MRR-ALL processing only        
  $$MAPDIR$$            - mAdb mapping file for JTV sample name processing only   

  prologMRR.html
  epilogueMRR.html

  prologJTV.html
  epilogueJTV.html

   java -Xmx256M -classpath .;.\HTMLtools.jar HTMLtools \
          data.GBS/params-genBatchScripts.map

EG1-test-1+FC.txt           EG1-test-1-FC.txt  (t-Test or fold-change test gene set)
EG1-test-1+FC-ALL.txt       EG1-test-1-FC-ALL.txt (AND of test gene set with ALL samples)
EG1-test-1+FC-JTV.zip       EG1-test-1-FC-JTV.zip   (JTV heatmap for gene set)
EG1-test-1+FC-JTV-ALL.zip   EG1-test-1-FC-JTV-ALL.zip   (JTV heatmap for ALL samples)

EG1-test-1+FC.txt            EG1-test-1-FC.txt (t-Test or fold-change gene set test)
EG1-test-1+FC-ALL.txt        EG1-test-1-FC-ALL.txt (AND of test gene set with ALL samples)
and
EG1-test-1+FC.html           EG1-test-1-FC.html (t-Test or F-C test - with expr.data)
EG1-test-1+FC-keep.html      EG1-test-1-FC-keep.html (t-Test or F-C test - no expr. data)
EG1-test-1+FC-ALL.html       EG1-test-1-FC-ALL.html (AND of test gene set with ALL samples)
EG1-test-1+FC-JTV.html       EG1-test-1-FC-JTV.html     (JTV heatmap for gene set)
EG1-test-1+FC-JTV-ALL.html   EG1-test-1-FC-JTV-ALL.html (JTV heatmap for ALL samples)
EG1-test-1+FC-JTV.zip        EG1-test-1-FC-JTV.zip      (JTV heatmap for gene set)
EG1-test-1+FC-JTV-ALL.zip    EG1-test-1-FC-JTV-ALL.zip  (JTV heatmap for ALL samples)

   java -Xmx512M -classpath .;.\HTMLtools.jar HTMLtools \
          -batchProcess:batchScripts/buildWebPages.doit

7.10. Converting data from GSP-Inventory for the Jak-Stat Prospector

7.10.1 HTMLtools distribution directory

  Data.GBS/             - GenBatchScripts to create batchScripts/ directory
  Data.GSPI-EG/         - EGxxxx.txt data, HTML and concatenated EGMAP.txt scripts 
  Data.GSPI-ExpGrp/     - ExperimentGroups.txt data and HTML scripts 
  Data.mAdb-TestsToDo/  - script to create HTML of mAdb-TestsToDo
  Data.Maps/            - the scripts used to create HTML and .map files
  JTVjars/              - the JTV runtime jar files required
  Data.Table/           - primary .txt and .map files for EGMAP, ExperimentGroups,
                          mAdbArraySummary, and mAdb-TestsToDo files

  batchScripts/         - the directory created when run GenBatchScripts
  html/                 - the directory created when run -batchProcess:batchList.doit
  JTVoutput/            - the JTV demonstration conversion output (from JTVinput/)

  Data.MRR/             - separate demonstration mAdb MRR conversions to HTML
  Data.MRR-all/         - fast-edit table conversion scripts using buffered I/O
  JTVinput/             - the JTV demonstration conversion scripts and data

  build/build.xml       - ANT build file for the making the converter 
  demo-bat/             - additional Windows BAT scripts in portable ("...-bat") form 
  docs/                 - additional converter documentation 
  javadocs/             - automatic javadoc Java documentation for the converter
  src/                  - source code for the HTMLtools converter

  HTMLtools.jar          - converter Java jar file used by the BAT scripts
  ReferenceManual.html   - primary documentation for the converter
  README-NOTE-restoring-the-BAT-file-names.txt - how to activate the BAT files

   java -Xm256M -classpath .;.\HTMLtools.jar HTMLtools \
        -batchProcessing:batchList.doit

It has been released with a small non-proprietary sample data currently publicly available on NCBI GEO to demonstrate some of the aspects of the software.

It was derived and refactored from the open source MAExplorer (http://maexplorer.sourceforge.net/), and Open2Dprot (http://Open2Dprot.sourceforge.net/) Table modules.

Copyright 2008, 2009 by Peter Lemkin E-Mail: lemkin@users.sourceforge.net http://lemkingroup.com