Mercurial > repos > devteam > picard
diff 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 |
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--- a/rgPicardASMetrics.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardASMetrics.xml Tue Apr 02 09:42:36 2013 -0400 @@ -1,10 +1,10 @@ <tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0"> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" - --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --datatype "$input_file.ext" + picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" + --assumesorted "${sorted}" -b "${bisulphite}" --adaptors "${adaptors}" --maxinsert "${maxinsert}" -n "${out_prefix}" --datatype "${input_file.ext}" -j \$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar --tmpdir "${__new_file_path__}" #if $genomeSource.refGenomeSource == "history": - --ref-file "$genomeSource.ownFile" + --ref-file "${genomeSource.ownFile}" #else --ref "${genomeSource.index.fields.path}" #end if