#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 ---------------"