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> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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