| Previous changeset 7:a1c96ef6c111 (2013-04-17) Next changeset 9:68db09d2e2a4 (2013-04-18) |
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Commit message:
Uploaded |
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modified:
RnBeadsGalaxy.R rnbeads_galaxy_wrapper.sh |
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added:
automated.option.assignments.txt |
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| 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 |
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| @@ -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) |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |