[galaxy-commits] commit/galaxy-central: fubar: Bumped ALL picard tool versions and made them uniformly 1.56.0 to reflect the current picard tools version Nate's about to unleash.

11 Nov 2011

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"

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: fubar: 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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