Mercurial > repos > devteam > picard
diff rgPicardMarkDups.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 |
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--- a/rgPicardMarkDups.xml Thu Oct 25 12:51:42 2012 -0400 +++ b/rgPicardMarkDups.xml Tue Apr 02 09:42:36 2013 -0400 @@ -1,8 +1,8 @@ <tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0"> <command interpreter="python"> - picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" - --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist" - -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext" + picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" -o "${out_file}" + --remdups "${remDups}" --assumesorted "${assumeSorted}" --readregex "${readRegex}" --optdupdist "${optDupeDist}" + -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "${html_file.files_path}" -t "${html_file}" -e "${input_file.ext}" </command> <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> <inputs>