# HG changeset patch
# User pavlo-lutsik
# Date 1366284996 14400
# Node ID 7bc6e673c8e8e85566efc18b95dbf5881ad48ad7
# Parent  a1c96ef6c111a1f23e7a3fdde39f44306fbf84e9
Uploaded

diff -r a1c96ef6c111 -r 7bc6e673c8e8 RnBeadsGalaxy.R
--- a/RnBeadsGalaxy.R	Wed Apr 17 08:45:05 2013 -0400
+++ b/RnBeadsGalaxy.R	Thu Apr 18 07:36:36 2013 -0400
@@ -41,7 +41,7 @@
 #			string
 #		})
 #
-#cat(xml.strings, sep="", file="C:\\Users\\User\\workspace\\RnBeads\\Supplement\\galaxy\\automated.settings.xml.txt")
+#cat(xml.strings, sep="", file="automated.settings.xml.txt")
 #
 #opt.def.strings<-apply(rnb.opt.spec,1, function(row){
 #			
@@ -52,12 +52,12 @@
 #			if(row[4]=="logical"){
 #				def.string<-sprintf("#if str( $options.%s ) == \"True\"\n\t--%s\n#end if\n", opt.name, opt.long)		
 #			}else{
-#				def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s = \"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name)
+#				def.string<-sprintf("#if str( $options.%s ) != \"\"\n\t--%s=\"$options.%s\" \n#end if\n", opt.name, opt.long, opt.name)
 #			}
 #			def.string
 #			
 #		})
-#cat(opt.def.strings, sep="", file="C:\\Users\\User\\workspace\\RnBeads\\Supplement\\galaxy\\automated.option.assignments.txt")
+#cat(opt.def.strings, sep="", file="automated.option.assignments.txt")
 
 
 rnb.opt.spec$Type<-gsub("\\.vector", "", rnb.opt.spec$Type)
diff -r a1c96ef6c111 -r 7bc6e673c8e8 automated.option.assignments.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/automated.option.assignments.txt	Thu Apr 18 07:36:36 2013 -0400
@@ -0,0 +1,210 @@
+				#if str( $options.analysisName ) != ""
+					--analysis-name="$options.analysisName" 
+				#end if
+				#if str( $options.logging ) == "True"
+					--logging
+				#end if
+				#if str( $options.email ) != ""
+					--email="$options.email" 
+				#end if
+				#if str( $options.assembly ) != ""
+					--assembly="$options.assembly" 
+				#end if
+				#if str( $options.analyzeSites ) == "True"
+					--analyze-sites
+				#end if
+				#if str( $options.regionTypes ) != ""
+					--region-types="$options.regionTypes" 
+				#end if
+				#if str( $options.identifiersColumn ) != ""
+					--identifiers-column="$options.identifiersColumn" 
+				#end if
+				#if str( $options.pointsCategory ) != ""
+					--points-category="$options.pointsCategory" 
+				#end if
+				#if str( $options.colorsCategory ) != ""
+					--colors-category="$options.colorsCategory" 
+				#end if
+				#if str( $options.colorsGradient ) != ""
+					--colors-gradient="$options.colorsGradient" 
+				#end if
+				#if str( $options.minGroupSize ) != ""
+					--min-group-size="$options.minGroupSize" 
+				#end if
+				#if str( $options.maxGroupCount ) != ""
+					--max-group-count="$options.maxGroupCount" 
+				#end if
+				#if str( $options.gzLargeFiles ) == "True"
+					--gz-large-files
+				#end if
+				#if str( $options.strandSpecific ) == "True"
+					--strand-specific
+				#end if
+				#if str( $options.replicateIdColumn ) != ""
+					--replicate-id-column="$options.replicateIdColumn" 
+				#end if
+				#if str( $options.loadingNormalization ) == "True"
+					--loading-normalization
+				#end if
+				#if str( $options.loadingDefaultDataType ) != ""
+					--loading-default-data-type="$options.loadingDefaultDataType" 
+				#end if
+				#if str( $options.loadingTableSeparator ) != ""
+					--loading-table-separator="$options.loadingTableSeparator" 
+				#end if
+				#if str( $options.loadingBedStyle ) != ""
+					--loading-bed-style="$options.loadingBedStyle" 
+				#end if
+				#if str( $options.loadingBedColumns ) != ""
+					--loading-bed-columns="$options.loadingBedColumns" 
+				#end if
+				#if str( $options.loadingBedFrameShift ) != ""
+					--loading-bed-frame-shift="$options.loadingBedFrameShift" 
+				#end if
+				#if str( $options.normalizationMethod ) != ""
+					--normalization-method="$options.normalizationMethod" 
+				#end if
+				#if str( $options.normalizationSubtractBackground ) == "True"
+					--normalization-subtract-background
+				#end if
+				#if str( $options.qc ) == "True"
+					--qc
+				#end if
+				#if str( $options.qcBoxplots ) == "True"
+					--qc-boxplots
+				#end if
+				#if str( $options.qcBarplots ) == "True"
+					--qc-barplots
+				#end if
+				#if str( $options.qcNegativeBoxplot ) == "True"
+					--qc-negative-boxplot
+				#end if
+				#if str( $options.qcSnpHeatmap ) == "True"
+					--qc-snp-heatmap
+				#end if
+				#if str( $options.qcSnpBoxplot ) == "True"
+					--qc-snp-boxplot
+				#end if
+				#if str( $options.qcSnpBarplot ) == "True"
+					--qc-snp-barplot
+				#end if
+				#if str( $options.qcSampleBatchSize ) != ""
+					--qc-sample-batch-size="$options.qcSampleBatchSize" 
+				#end if
+				#if str( $options.filteringContextRemoval ) != ""
+					--filtering-context-removal="$options.filteringContextRemoval" 
+				#end if
+				#if str( $options.filteringSnp ) == "True"
+					--filtering-snp
+				#end if
+				#if str( $options.filteringSnpFrequency ) != ""
+					--filtering-snp-frequency="$options.filteringSnpFrequency" 
+				#end if
+				#if str( $options.filteringSnpAccepted ) != ""
+					--filtering-snp-accepted="$options.filteringSnpAccepted" 
+				#end if
+				#if str( $options.filteringSexChromosomesRemoval ) == "True"
+					--filtering-sex-chromosomes-removal
+				#end if
+				#if str( $options.filteringMissingValueQuantile ) != ""
+					--filtering-missing-value-quantile="$options.filteringMissingValueQuantile" 
+				#end if
+				#if str( $options.filteringCoverageThreshold ) != ""
+					--filtering-coverage-threshold="$options.filteringCoverageThreshold" 
+				#end if
+				#if str( $options.filteringLowCoverageMasking ) == "True"
+					--filtering-low-coverage-masking
+				#end if
+				#if str( $options.filteringHighCoverageOutliers ) == "True"
+					--filtering-high-coverage-outliers
+				#end if
+				#if str( $options.filteringGreedycut ) == "True"
+					--filtering-greedycut
+				#end if
+				#if str( $options.filteringGreedycutPvalueThreshold ) != ""
+					--filtering-greedycut-pvalue-threshold="$options.filteringGreedycutPvalueThreshold" 
+				#end if
+				#if str( $options.filteringGreedycutRcTies ) != ""
+					--filtering-greedycut-rc-ties="$options.filteringGreedycutRcTies" 
+				#end if
+				#if str( $options.filteringDeviationThreshold ) != ""
+					--filtering-deviation-threshold="$options.filteringDeviationThreshold" 
+				#end if
+				#if str( $options.batch ) == "True"
+					--batch
+				#end if
+				#if str( $options.batchDreductionColumns ) != ""
+					--batch-dreduction-columns="$options.batchDreductionColumns" 
+				#end if
+				#if str( $options.batchPrincipalComponents ) != ""
+					--batch-principal-components="$options.batchPrincipalComponents" 
+				#end if
+				#if str( $options.batchCorrelationColumns ) != ""
+					--batch-correlation-columns="$options.batchCorrelationColumns" 
+				#end if
+				#if str( $options.batchCorrelationPvalueThreshold ) != ""
+					--batch-correlation-pvalue-threshold="$options.batchCorrelationPvalueThreshold" 
+				#end if
+				#if str( $options.batchCorrelationPermutations ) != ""
+					--batch-correlation-permutations="$options.batchCorrelationPermutations" 
+				#end if
+				#if str( $options.batchCorrelationQc ) == "True"
+					--batch-correlation-qc
+				#end if
+				#if str( $options.profiles ) == "True"
+					--profiles
+				#end if
+				#if str( $options.profilesBetaDistribution ) == "True"
+					--profiles-beta-distribution
+				#end if
+				#if str( $options.profilesIntersample ) == "True"
+					--profiles-intersample
+				#end if
+				#if str( $options.profilesDeviationPlots ) == "True"
+					--profiles-deviation-plots
+				#end if
+				#if str( $options.profilesColumns ) != ""
+					--profiles-columns="$options.profilesColumns" 
+				#end if
+				#if str( $options.profilesClustering ) == "True"
+					--profiles-clustering
+				#end if
+				#if str( $options.profilesClusteringTopProbes ) != ""
+					--profiles-clustering-top-probes="$options.profilesClusteringTopProbes" 
+				#end if
+				#if str( $options.regionProfilesTypes ) != ""
+					--region-profiles-types="$options.regionProfilesTypes" 
+				#end if
+				#if str( $options.differential ) == "True"
+					--differential
+				#end if
+				#if str( $options.differentialPermutations ) != ""
+					--differential-permutations="$options.differentialPermutations" 
+				#end if
+				#if str( $options.differentialComparisonColumns ) != ""
+					--differential-comparison-columns="$options.differentialComparisonColumns" 
+				#end if
+				#if str( $options.differentialEnrichment ) == "True"
+					--differential-enrichment
+				#end if
+				#if str( $options.exportToUcsc ) != ""
+					--export-to-ucsc="$options.exportToUcsc" 
+				#end if
+				#if str( $options.exportToBed ) == "True"
+					--export-to-bed
+				#end if
+				#if str( $options.exportToCsv ) == "True"
+					--export-to-csv
+				#end if
+				#if str( $options.exportTypes ) != ""
+					--export-types="$options.exportTypes" 
+				#end if
+				#if str( $options.colors3Gradient ) != ""
+					--colors-3-gradient="$options.colors3Gradient" 
+				#end if
+				#if str( $options.loggingMemory ) == "True"
+					--logging-memory
+				#end if
+				#if str( $options.usePstoimg ) == "True"
+					--use-pstoimg
+				#end if
\ No newline at end of file
diff -r a1c96ef6c111 -r 7bc6e673c8e8 rnbeads_galaxy_wrapper.sh
--- a/rnbeads_galaxy_wrapper.sh	Wed Apr 17 08:45:05 2013 -0400
+++ b/rnbeads_galaxy_wrapper.sh	Thu Apr 18 07:36:36 2013 -0400
@@ -1,4 +1,5 @@
 #!/bin/bash
 
-Rscript --slave $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $*
-#Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $*
\ No newline at end of file
+Rscript --slave $(dirname $(readlink -f $0))/RnBeadsGalaxy.R $* > RnBeads.out
+#Rscript --no-save \$R_SCRIPTS_PATH/RnBeadsGalaxy.R $*
+exit 0
\ No newline at end of file