#File:"$$PARAM_MAP_NAME$$" #"Generate a Tests-Intersection Table and HTML" #"Standard Tests-Intersection processing" #"Revised: 5-6-2009" #"GBS: $$DATE$$" # #"[1] Master script to create a Tests Intersection Table file for all tests" #"in the mAdb-TestsToDo.txt file that we have data." # -inputDir:$$INPUT_DATA$$ -outputDir:$$OUTPUT_DATA$$ # #"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." -tableDir:$$TABLE_DATA$$ # -allowHdrDups -rmvTrailingBlankRowsAndColumns -hdrLines:2 -hasEmptyLineBeforeTable # -makeTestsIntersectionTable:"$$TESTS-TODO-FILE.2$$" # -filterTestTestIntersection:"Relative directory,$$TISSUE.2$$" ###-filterTestTestIntersection:"HTML page label,$$FILTER_TI_TEST_LIST$$" # #"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:"Tests-Intersection-$$TISSUE.2$$.txt,HTML" # #"[2] Now after the Tests-Intersection .txt table is saved, generate the HTML file." #"Note: Converter removes -hasEmptyLineBeforeTable and sets -hdrLines:5 switches." # -mapDollarsigns:$$TISSUE$$,"$$TISSUE.2$$" -mapDollarsigns:$$TESTS-TODO-FILE$$,"$$TESTS-TODO-FILE.2$$" # -addPrologue:"$$PROLOG-TI$$" -addEpilogue:"$$EPILOGUE-TI$$" # -addRowNumbers -addTableName:"Intersection of All $$TISSUE.2$$ GSP Fold-Change Tests" -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 ---------------"