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comparison rgPicardLibComplexity.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
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1:e0232cbac965 2:9227b8c3093b
1 <tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0"> 1 <tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0">
2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> 2 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
3 <command interpreter="python"> 3 <command interpreter="python">
4 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" 4 picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --minid "${minIDbases}"
5 --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" 5 --maxdiff "${maxDiff}" --minmeanq "${minMeanQ}" --readregex "${readRegex}" --optdupdist "${optDupeDist}"
6 -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file" 6 -j "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "${html_file.files_path}" -t "${html_file}"
7 </command> 7 </command>
8 <inputs> 8 <inputs>
9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset" 9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset"
10 help="If empty, upload or import a SAM/BAM dataset."/> 10 help="If empty, upload or import a SAM/BAM dataset."/>
11 <param name="out_prefix" value="Library Complexity" type="text" 11 <param name="out_prefix" value="Library Complexity" type="text"