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Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.

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This commit is contained in:
Ross Lazarus
2011-11-12 04:25:19 +11:00
parent c39d191e20
commit a6719bff5d
14 changed files with 14 additions and 14 deletions
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tools/picard/picard_AddOrReplaceReadGroups.xml
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<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.1">
<tool name="Add or Replace Groups" id="picard_ARRG" version="1.56.0">
<requirements><requirement type="package">picard</requirement></requirements>
<command interpreter="python">
picard_wrapper.py
tools/picard/picard_BamIndexStats.xml
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<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.1">
<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0">
<requirements><requirement type="package">picard</requirement></requirements>
<command interpreter="python">
picard_wrapper.py
tools/picard/picard_FastqToSam.xml
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<tool id="picard_FastqToSam" name="FASTQ to BAM" version="0.0.1">
<tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">
<description>creates an unaligned BAM file</description>
<requirements><requirement type="package">picard</requirement></requirements>
<command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
tools/picard/picard_MarkDuplicates.xml
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@@ -1,4 +1,4 @@
<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01.1">
<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="1.56.0">
<command interpreter="python">
picard_wrapper.py
--input="$input_file"
tools/picard/picard_ReorderSam.xml
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@@ -1,4 +1,4 @@
<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.1">
<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">
<requirements><requirement type="package">picard</requirement></requirements>
<command interpreter="python">
picard_wrapper.py
tools/picard/picard_ReplaceSamHeader.xml
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@@ -1,4 +1,4 @@
<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.1">
<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0">
<requirements><requirement type="package">picard</requirement></requirements>
<command interpreter="python">
picard_wrapper.py
tools/picard/picard_SamToFastq.xml
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<tool id="picard_SamToFastq" name="SAM to FASTQ" version="0.0.1">
<tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.0">
<description>creates a FASTQ file</description>
<requirements><requirement type="package">picard</requirement></requirements>
<command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
tools/picard/rgPicardASMetrics.xml
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<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1">
<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0">
<command interpreter="python">
picard_wrapper.py -i "$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"
tools/picard/rgPicardFixMate.xml
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<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.1">
<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"
tools/picard/rgPicardGCBiasMetrics.xml
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<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02.1">
<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 "${__new_file_path__}"
tools/picard/rgPicardHsMetrics.xml
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<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02.1">
<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0">
<description>for targeted resequencing data</description>
<command interpreter="python">
tools/picard/rgPicardInsertSize.xml
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<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.2">
<tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0">
<description>for PAIRED data</description>
<requirements><requirement type="package">picard</requirement></requirements>
<command interpreter="python">
tools/picard/rgPicardLibComplexity.xml
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<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01.1">
<tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0">
<command interpreter="python">
picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases"
--maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist"
tools/picard/rgPicardMarkDups.xml
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<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01.1">
<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0">
<command interpreter="python">
picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file"
--remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist"