Mercurial > repos > devteam > picard
comparison rgPicardASMetrics.xml @ 2:9227b8c3093b
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 |
comparison
equal
deleted
inserted
replaced
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> |