#File:"$$PARAM_MAP_NAME$$"
#"Standard MRR processing with no HTML generated, but the converted table saved."
#"Revised: 4-12-2009"
#"GBS: $$DATE$$"
#
-addRowNumbers
-inputDir:$$INPUT_DATA$$
-outputDir:$$OUTPUT_DATA$$
-tablesDir:$$TABLE_DATA$$
-files:"$$FILES$$"
#
-allowHdrDups
-alternateRowBackgroundColor:white
-rmvTrailingBlankRowsAndColumns
#-shrinkBigCells:25,-5
-shrinkBigCells:1,-5
-hdrLines:2
-hasEmptyLineBeforeTable
#
#"Save the edited table as a .txt file"
-saveEditedTable2File:,noHTML
#
#"Map header names. Select  from field='Affy .CEL file (16)'"
#"  to field= 'GSP ID (9)' or 'Simple GSP ID (10)'" 
-mapHdrNames:"$$TABLE_DATA$$/EGMAP.map,Affy .CEL file (16),GSP ID (9)"
#
#"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 the remaining columns alphabetically"
-reorderRemainingColumnsAlphabeticly
#
#"Sort rows by column - use whichever comes first"
-sortRowsByColumn:"A-B Mean Difference",Descending
-sortRowsByColumn:Difference,Descending
-sortRowsByColumn:p-Value,Ascending
-sortRowsByColumn:Gene,Ascending
#
#"----------- End ---------- "