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comparison rgPicardASMetrics.xml @ 2:9227b8c3093b

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Updated command line format per dev team standards.
author devteam <devteam@galaxyproject.org>
date Tue, 02 Apr 2013 09:42:36 -0400
parents 1cd7f3b42609
children ab1f60c26526
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1:e0232cbac965 2:9227b8c3093b
1 <tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0"> 1 <tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0">
2 <command interpreter="python"> 2 <command interpreter="python">
3 picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" 3 picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
4 --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext" 4 --assumesorted "${sorted}" -b "${bisulphite}" --adaptors "${adaptors}" --maxinsert "${maxinsert}" -n "${out_prefix}" --datatype "${input_file.ext}"
5 -j \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar --tmpdir "${__new_file_path__}" 5 -j \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar --tmpdir "${__new_file_path__}"
6 #if $genomeSource.refGenomeSource == "history": 6 #if $genomeSource.refGenomeSource == "history":
7 --ref-file "$genomeSource.ownFile" 7 --ref-file "${genomeSource.ownFile}"
8 #else 8 #else
9 --ref "${genomeSource.index.fields.path}" 9 --ref "${genomeSource.index.fields.path}"
10 #end if 10 #end if
11 </command> 11 </command>
12 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> 12 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>