1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/744902bbb2b9/ changeset: 744902bbb2b9 user: fubar date: 2011-11-11 18:25:19 summary: Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash. affected #: 14 files

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/picard_AddOrReplaceReadGroups.xml --- a/tools/picard/picard_AddOrReplaceReadGroups.xml +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml @@ -1,4 +1,4 @@ -<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

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/picard_BamIndexStats.xml --- a/tools/picard/picard_BamIndexStats.xml +++ b/tools/picard/picard_BamIndexStats.xml @@ -1,4 +1,4 @@ -<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

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/picard_FastqToSam.xml --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -1,4 +1,4 @@ -<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

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/picard_MarkDuplicates.xml --- a/tools/picard/picard_MarkDuplicates.xml +++ b/tools/picard/picard_MarkDuplicates.xml @@ -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"

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/picard_ReorderSam.xml --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -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

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/picard_ReplaceSamHeader.xml --- a/tools/picard/picard_ReplaceSamHeader.xml +++ b/tools/picard/picard_ReplaceSamHeader.xml @@ -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

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/picard_SamToFastq.xml --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -1,4 +1,4 @@ -<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

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -1,4 +1,4 @@ -<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"

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/rgPicardFixMate.xml --- a/tools/picard/rgPicardFixMate.xml +++ b/tools/picard/rgPicardFixMate.xml @@ -1,4 +1,4 @@ -<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"

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/rgPicardGCBiasMetrics.xml --- a/tools/picard/rgPicardGCBiasMetrics.xml +++ b/tools/picard/rgPicardGCBiasMetrics.xml @@ -1,4 +1,4 @@ -<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__}"

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/rgPicardHsMetrics.xml --- a/tools/picard/rgPicardHsMetrics.xml +++ b/tools/picard/rgPicardHsMetrics.xml @@ -1,4 +1,4 @@ -<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">

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/rgPicardInsertSize.xml --- a/tools/picard/rgPicardInsertSize.xml +++ b/tools/picard/rgPicardInsertSize.xml @@ -1,4 +1,4 @@ -<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">

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/rgPicardLibComplexity.xml --- a/tools/picard/rgPicardLibComplexity.xml +++ b/tools/picard/rgPicardLibComplexity.xml @@ -1,4 +1,4 @@ -<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"

diff -r 0474dfc4d30f0d77aac42f1a0a8355998f213bfd -r 744902bbb2b94202f361f962f626e95a2bc18111 tools/picard/rgPicardMarkDups.xml --- a/tools/picard/rgPicardMarkDups.xml +++ b/tools/picard/rgPicardMarkDups.xml @@ -1,4 +1,4 @@ -<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"

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