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comparison rgPicardInsertSize.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="Insertion size metrics" id="PicardInsertSize" version="1.56.0"> 1 <tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0">
2 <description>for PAIRED data</description> 2 <description>for PAIRED data</description>
3 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> 3 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
4 <command interpreter="python"> 4 <command interpreter="python">
5 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations" 5 picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --deviations "${deviations}"
6 --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel" 6 --histwidth "${histWidth}" --minpct "${minPct}" --malevel "${malevel}"
7 -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" 7 -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "${html_file.files_path}" -t "${html_file}"
8 </command> 8 </command>
9 <inputs> 9 <inputs>
10 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" 10 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
11 help="If empty, upload or import a SAM/BAM dataset."/> 11 help="If empty, upload or import a SAM/BAM dataset."/>
12 <param name="out_prefix" value="Insertion size metrics" type="text" 12 <param name="out_prefix" value="Insertion size metrics" type="text"