commit/galaxy-central: dan: Update Picard tools to use tool-data/shared/jars/picard/* instead of just tool-data/shared/jars/*. - galaxy-commits

25 Oct 2011

1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/18f2b18d48e8/
changeset:   18f2b18d48e8
user:        dan
date:        2011-10-25 16:34:35
summary:     Update Picard tools to use tool-data/shared/jars/picard/* instead of just tool-data/shared/jars/*.
affected #:  14 files
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef 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="0.2.0">
+<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python">
     picard_wrapper.py
@@ -15,7 +15,7 @@
       #end if
       --output-format=$outputFormat
       --output=$outFile
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/AddOrReplaceReadGroups.jar"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/AddOrReplaceReadGroups.jar"
   </command><inputs><param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in"
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef 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="0.2.0">
+<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python">
     picard_wrapper.py
@@ -6,7 +6,7 @@
       --bai-file "$input_file.metadata.bam_index"
       -t "$htmlfile"
       -d "$htmlfile.files_path"
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/BamIndexStats.jar"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/BamIndexStats.jar"
   </command><inputs><param format="bam" name="input_file" type="data"  label="BAM dataset to generate statistics for"
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_FastqToSam.xml
--- a/tools/picard/picard_FastqToSam.xml
+++ b/tools/picard/picard_FastqToSam.xml
@@ -1,5 +1,6 @@
 <tool id="picard_FastqToSam" name="FASTQ to BAM" version="0.0.1"><description>creates an unaligned BAM file</description>
+  <requirements><requirement type="package">picard</requirement></requirements><command>java  -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar"
     FASTQ="${input_fastq1}"
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_MarkDuplicates.xml
--- a/tools/picard/picard_MarkDuplicates.xml
+++ b/tools/picard/picard_MarkDuplicates.xml
@@ -1,4 +1,4 @@
-<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01">
+<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01.1"><command interpreter="python">
     picard_wrapper.py
       --input="$input_file"
@@ -20,7 +20,7 @@
           --output-sam=$outFileBamMarked
         #end if
       #end if
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/"
       --picard-cmd="MarkDuplicates"
   </command><inputs>
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_ReorderSam.xml
--- a/tools/picard/picard_ReorderSam.xml
+++ b/tools/picard/picard_ReorderSam.xml
@@ -1,4 +1,4 @@
-<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.0">
+<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python">
     picard_wrapper.py
@@ -15,7 +15,7 @@
       --allow-contig-len-discord=$allowContigLenDiscord
       --output-format=$outputFormat
       --output=$outFile
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReorderSam.jar"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReorderSam.jar"
   </command><inputs><param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef 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="0.2.0">
+<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python">
     picard_wrapper.py
@@ -6,7 +6,7 @@
       -o $outFile
       --header-file $headerFile
       --output-format $outputFormat
-      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReplaceSamHeader.jar"
+      -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReplaceSamHeader.jar"
       --tmpdir "${__new_file_path__}" 
   </command><inputs>
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_SamToFastq.xml
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -1,5 +1,6 @@
 <tool id="picard_SamToFastq" name="SAM to FASTQ" version="0.0.1"><description>creates a FASTQ file</description>
+  <requirements><requirement type="package">picard</requirement></requirements><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
     -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar"
     INPUT="${input_sam}"
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardASMetrics.xml
--- a/tools/picard/rgPicardASMetrics.xml
+++ b/tools/picard/rgPicardASMetrics.xml
@@ -1,8 +1,8 @@
-<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03">
+<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1"><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"
-    -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectAlignmentSummaryMetrics.jar
+    -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar
 #if $genomeSource.refGenomeSource == "history":
     --ref-file "$genomeSource.ownFile"
 #else
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardFixMate.xml
--- a/tools/picard/rgPicardFixMate.xml
+++ b/tools/picard/rgPicardFixMate.xml
@@ -1,8 +1,8 @@
-<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.0">
+<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.1"><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 "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/FixMateInformation.jar" --sortorder "$sortOrder"
+   --output-format "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FixMateInformation.jar" --sortorder "$sortOrder"
   </command><requirements><requirement type="package">picard</requirement></requirements><inputs>
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardGCBiasMetrics.xml
--- a/tools/picard/rgPicardGCBiasMetrics.xml
+++ b/tools/picard/rgPicardGCBiasMetrics.xml
@@ -1,8 +1,8 @@
-<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02">
+<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02.1"><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 ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectGcBiasMetrics.jar
+    -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectGcBiasMetrics.jar
 #if $genomeSource.refGenomeSource == "history":
  --ref-file "$genomeSource.ownFile"
 #else:
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardHsMetrics.xml
--- a/tools/picard/rgPicardHsMetrics.xml
+++ b/tools/picard/rgPicardHsMetrics.xml
@@ -1,10 +1,10 @@
-<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02">
+<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02.1"><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__}"
-    -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CalculateHsMetrics.jar"
+    -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CalculateHsMetrics.jar"
</command><requirements><requirement type="package">picard</requirement></requirements>
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardInsertSize.xml
--- a/tools/picard/rgPicardInsertSize.xml
+++ b/tools/picard/rgPicardInsertSize.xml
@@ -1,10 +1,10 @@
-<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.0">
+<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.1"><description>for PAIRED data</description><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python">
    picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit"
    --histwidth "$histWidth" --minpct "$minPct"
-   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
+   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/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"
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardLibComplexity.xml
--- a/tools/picard/rgPicardLibComplexity.xml
+++ b/tools/picard/rgPicardLibComplexity.xml
@@ -1,8 +1,8 @@
-<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01">
+<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01.1"><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 "${GALAXY_DATA_INDEX_DIR}/shared/jars/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file"
+   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/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"
diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardMarkDups.xml
--- a/tools/picard/rgPicardMarkDups.xml
+++ b/tools/picard/rgPicardMarkDups.xml
@@ -1,8 +1,8 @@
-<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01">
+<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01.1"><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 "${GALAXY_DATA_INDEX_DIR}/shared/jars/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext"
+   -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext"
   </command><requirements><requirement type="package">picard</requirement></requirements><inputs>
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