| Previous changeset 1:e0232cbac965 (2012-10-25) Next changeset 3:bf1c3f9f8282 (2013-05-03) |
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Commit message:
Updated command line format per dev team standards. |
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modified:
picard_AddOrReplaceReadGroups.xml picard_BamIndexStats.xml picard_ReorderSam.xml picard_ReplaceSamHeader.xml picard_SamToFastq.xml rgPicardASMetrics.xml rgPicardFixMate.xml rgPicardGCBiasMetrics.xml rgPicardHsMetrics.xml rgPicardInsertSize.xml rgPicardLibComplexity.xml rgPicardMarkDups.xml |
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| diff -r e0232cbac965 -r 9227b8c3093b picard_AddOrReplaceReadGroups.xml --- a/picard_AddOrReplaceReadGroups.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/picard_AddOrReplaceReadGroups.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -2,19 +2,19 @@ <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <command interpreter="python"> picard_wrapper.py - --input="$inputFile" - --rg-lb="$rglb" - --rg-pl="$rgpl" - --rg-pu="$rgpu" - --rg-sm="$rgsm" - --rg-id="$rgid" - --rg-opts=${readGroupOpts.rgOpts} + --input="${inputFile}" + --rg-lb="${rglb}" + --rg-pl="${rgpl}" + --rg-pu="${rgpu}" + --rg-sm="${rgsm}" + --rg-id="${rgid}" + --rg-opts="${readGroupOpts.rgOpts}" #if $readGroupOpts.rgOpts == "full" - --rg-cn="$readGroupOpts.rgcn" - --rg-ds="$readGroupOpts.rgds" + --rg-cn="${readGroupOpts.rgcn}" + --rg-ds="${readGroupOpts.rgds}" #end if - --output-format=$outputFormat - --output=$outFile + --output-format="${outputFormat}" + --output="${outFile}" -j "\$JAVA_JAR_PATH/AddOrReplaceReadGroups.jar" --tmpdir "${__new_file_path__}" </command> |
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| diff -r e0232cbac965 -r 9227b8c3093b picard_BamIndexStats.xml --- a/picard_BamIndexStats.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/picard_BamIndexStats.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -2,10 +2,10 @@ <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <command interpreter="python"> picard_wrapper.py - --input "$input_file" - --bai-file "$input_file.metadata.bam_index" - -t "$htmlfile" - -d "$htmlfile.files_path" + --input "${input_file}" + --bai-file "${input_file.metadata.bam_index}" + -t "${htmlfile}" + -d "${htmlfile.files_path}" -j "\$JAVA_JAR_PATH/BamIndexStats.jar" --tmpdir "${__new_file_path__}" </command> |
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| diff -r e0232cbac965 -r 9227b8c3093b picard_ReorderSam.xml --- a/picard_ReorderSam.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/picard_ReorderSam.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -2,19 +2,19 @@ <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <command interpreter="python"> picard_wrapper.py - --input=$inputFile + --input="${inputFile}" #if $source.indexSource == "built-in" --ref="${source.ref.fields.path}" #else - --ref-file=$refFile - --species-name=$source.speciesName - --build-name=$source.buildName - --trunc-names=$source.truncateSeqNames + --ref-file="${refFile}" + --species-name="${source.speciesName}" + --build-name="${source.buildName}" + --trunc-names="${source.truncateSeqNames}" #end if - --allow-inc-dict-concord=$allowIncDictConcord - --allow-contig-len-discord=$allowContigLenDiscord - --output-format=$outputFormat - --output=$outFile + --allow-inc-dict-concord="${allowIncDictConcord}" + --allow-contig-len-discord="${allowContigLenDiscord}" + --output-format="${outputFormat}" + --output="${outFile}" --tmpdir "${__new_file_path__}" -j "\$JAVA_JAR_PATH/ReorderSam.jar" </command> |
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| diff -r e0232cbac965 -r 9227b8c3093b picard_ReplaceSamHeader.xml --- a/picard_ReplaceSamHeader.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/picard_ReplaceSamHeader.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -2,10 +2,10 @@ <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <command interpreter="python"> picard_wrapper.py - --input "$inputFile" - -o $outFile - --header-file $headerFile - --output-format $outputFormat + --input "${inputFile}" + -o "${outFile}" + --header-file "${headerFile}" + --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar" --tmpdir "${__new_file_path__}" </command> |
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| diff -r e0232cbac965 -r 9227b8c3093b picard_SamToFastq.xml --- a/picard_SamToFastq.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/picard_SamToFastq.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -8,8 +8,8 @@ -jar "\$JAVA_JAR_PATH/SamToFastq.jar" INPUT="${input_sam}" VALIDATION_STRINGENCY="LENIENT" - RE_REVERSE=${re_reverse} - INCLUDE_NON_PF_READS=${include_non_pf_reads} + RE_REVERSE="${re_reverse}" + INCLUDE_NON_PF_READS="${include_non_pf_reads}" #if str( $clipping_attribute ): CLIPPING_ATTRIBUTE="${clipping_attribute}" #end if @@ -22,7 +22,7 @@ #if str( $read1_max_bases_to_write ): READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}" #end if - INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments} + INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}" #if str( $output_per_read_group_selector ) == 'per_sam_file': ##OUTPUT_PER_RG=false @@ -54,7 +54,7 @@ #end if ' --read_group_file_1 "${output_fastq1}" - --new_files_path "${$__new_file_path__}" + --new_files_path "${__new_file_path__}" --file_id_1 "${output_fastq1.id}" #end if </command> |
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| diff -r e0232cbac965 -r 9227b8c3093b rgPicardASMetrics.xml --- a/rgPicardASMetrics.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardASMetrics.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -1,10 +1,10 @@ <tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0"> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" - --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext" + picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" + --assumesorted "${sorted}" -b "${bisulphite}" --adaptors "${adaptors}" --maxinsert "${maxinsert}" -n "${out_prefix}" --datatype "${input_file.ext}" -j \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar --tmpdir "${__new_file_path__}" #if $genomeSource.refGenomeSource == "history": - --ref-file "$genomeSource.ownFile" + --ref-file "${genomeSource.ownFile}" #else --ref "${genomeSource.index.fields.path}" #end if |
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| diff -r e0232cbac965 -r 9227b8c3093b rgPicardFixMate.xml --- a/rgPicardFixMate.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardFixMate.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -1,8 +1,8 @@ <tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0"> <description>for paired data</description> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" - --output-format "$outputFormat" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "$sortOrder" + picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}" + --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}" </command> <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <inputs> |
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| diff -r e0232cbac965 -r 9227b8c3093b rgPicardGCBiasMetrics.xml --- a/rgPicardGCBiasMetrics.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardGCBiasMetrics.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -1,8 +1,8 @@ <tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="1.56.0"> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" - --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" - -j \$JAVA_JAR_PATH/CollectGcBiasMetrics.jar + picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" + --windowsize "${windowsize}" --mingenomefrac "${mingenomefrac}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" + -j "\$JAVA_JAR_PATH/CollectGcBiasMetrics.jar" #if $genomeSource.refGenomeSource == "history": --ref-file "${genomeSource.ownFile}" #else: |
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| diff -r e0232cbac965 -r 9227b8c3093b rgPicardHsMetrics.xml --- a/rgPicardHsMetrics.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardHsMetrics.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -2,8 +2,8 @@ <description>for targeted resequencing data</description> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext" - --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}" + picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" --datatype "${input_file.ext}" + --baitbed "${bait_bed}" --targetbed "${target_bed}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" -j "\$JAVA_JAR_PATH/CalculateHsMetrics.jar" </command> |
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| diff -r e0232cbac965 -r 9227b8c3093b rgPicardInsertSize.xml --- a/rgPicardInsertSize.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardInsertSize.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -2,9 +2,9 @@ <description>for PAIRED data</description> <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations" - --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel" - -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" + picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --deviations "${deviations}" + --histwidth "${histWidth}" --minpct "${minPct}" --malevel "${malevel}" + -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "${html_file.files_path}" -t "${html_file}" </command> <inputs> <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" |
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| diff -r e0232cbac965 -r 9227b8c3093b rgPicardLibComplexity.xml --- a/rgPicardLibComplexity.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardLibComplexity.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -1,9 +1,9 @@ <tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0"> <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" - --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" - -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file" + picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --minid "${minIDbases}" + --maxdiff "${maxDiff}" --minmeanq "${minMeanQ}" --readregex "${readRegex}" --optdupdist "${optDupeDist}" + -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "${html_file.files_path}" -t "${html_file}" </command> <inputs> <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset" |
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| diff -r e0232cbac965 -r 9227b8c3093b rgPicardMarkDups.xml --- a/rgPicardMarkDups.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardMarkDups.xml Tue Apr 02 09:42:36 2013 -0400 |
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| @@ -1,8 +1,8 @@ <tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0"> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" - --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist" - -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext" + picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" -o "${out_file}" + --remdups "${remDups}" --assumesorted "${assumeSorted}" --readregex "${readRegex}" --optdupdist "${optDupeDist}" + -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "${html_file.files_path}" -t "${html_file}" -e "${input_file.ext}" </command> <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <inputs> |