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comparison rgPicardGCBiasMetrics.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 GC Bias Metrics" id="PicardGCBiasMetrics" version="1.56.0"> 1 <tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" 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 --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" 4 --windowsize "${windowsize}" --mingenomefrac "${mingenomefrac}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"
5 -j \$JAVA_JAR_PATH/CollectGcBiasMetrics.jar 5 -j "\$JAVA_JAR_PATH/CollectGcBiasMetrics.jar"
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