HTMLtools - A Web Page Conversion Tool Set

For example, it can convert a directory of tab-delimited files such as might be produced by Excel, various data analysis or database programs into a directory of HTML <TABLE> formated files. There are various commands available to make the table easier to read, including: Web page HTML preface and epilogue Web pages tailored to each data input file, shrinking large cells or moving content to additional pages, mapping cells to URL links associated with the column headers, alternating row colors, bolding headers, reconfiguring the table to keep or drop specified columns, reorder columns, sort rows by a particular column, remove trailing empty rows and columns, keyword mapping (date, filename, and user specified keywords), extract a sub-table by current table column keyword from a resource table file to insert into the prolog or epilogue section in a user specified format, sort rows by column data, etc. The program has a command line interface and can be launched with a simple command line invocation of a list of switches or can be run from a Windows BAT file or MacOS/Unix shell script. Multiple command switches can be specified in a script file that may be run as if they were typed on the command line. In addition, a list of script files may be specified in a batch file that then sequentially performs the converions - one for each script file mentioned in the list. The Reference Manual describes these options in detail as well as showing samples of input data and the generated output Web pages.

HTMLtools was originally called CvtTabDelim2HTML and was used to create Web pages for the Jak-Stat Prospector Web site part of the Trans-NIH Jak-Stat Initiative at http://jak-stat.nih.gov/ (currently a password-protected site for NIH-only access because some of the samples data has not released yet in the NLM/NCBI GEO database. However, some of the data is publicly available on GEO and we use that data in the examples for HTMLtools download distribution.

Conversions consist of a set of command line switches that map appear in a script input file on separate lines. A batch processing command -batchProcess in turn can have it execute a script containing any number of these separate conversion scripts. A sampling of the some of the types of commands includes:

Table editing

• Drop or keep specified columns.
• Reorder specific columns.
• Join data from several tables.
• Sort columns by specified column data.
• Reorder remaining columns by column names.
• Synthesize a Tests-Intersection table from a set of tests results tables.
• Fast table file editing (drop, keep reorder, etc.) for very large files.
• Save edited tables as tab-delimited data files instead of HTML (or do both).
• Handles multi-line headers and multi-table files.

HTML Web page generation

• Insert prolog and epilogue information in the HTML.
• Map data in specified columns to URL-linked entries.
• Generate hyperlinks for multi-line header tables.
• Map keyword names to using a (converter generated) mapping table resource database.
• Shrink table cell text size by the maximum number of characters/cell by either specifying a smaller <FONT> size or exporting the full text to a small linked HTML file.
• Extract a key-driven data row from an another file table and convert it to a DL, OL, UL or TABLE set of HTML syntax when doing keyword mapping in Web page generation.

Batch processing

• Specify command-line switches in a parameter script file that can be launched with a single command.
• Process a file of a list of conversion script files.
• Generate batch scripts for further processing using a database table to read a tree of input data, batch templates, mapping data, HTML templates etc. for subsequent running as a -batchProcess batch job to generate an output HTML tree suitable for copying to a Web server.

Do specialized search with Graphical User Interface (SearchGui) for generated index tables

• Perform specialized open ended searches of specialized Gene/probe ID for sets of processed normalized Affymetrix array data to generate HTML tables including a color heatmap option.
• Option to display fold-change values for subsets of the samples with optional fold-change thresholding to limit the amount of data data shown in the report..

See the Reference Manual for other conversion commands and command modifiers. For more information on the SearchGUI program, see the SearchGUI Manual for details.

About HTMLtools