Mercurial > repos > devteam > picard
comparison rgPicardMarkDups.xml @ 2:9227b8c3093b
Updated command line format per dev team standards.
author | devteam <devteam@galaxyproject.org> |
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date | Tue, 02 Apr 2013 09:42:36 -0400 |
parents | 1cd7f3b42609 |
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1:e0232cbac965 | 2:9227b8c3093b |
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1 <tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0"> | 1 <tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0"> |
2 <command interpreter="python"> | 2 <command interpreter="python"> |
3 picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" | 3 picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" -o "${out_file}" |
4 --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist" | 4 --remdups "${remDups}" --assumesorted "${assumeSorted}" --readregex "${readRegex}" --optdupdist "${optDupeDist}" |
5 -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext" | 5 -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "${html_file.files_path}" -t "${html_file}" -e "${input_file.ext}" |
6 </command> | 6 </command> |
7 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | 7 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> |
8 <inputs> | 8 <inputs> |
9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to mark duplicates in" | 9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to mark duplicates in" |
10 help="If empty, upload or import a SAM/BAM dataset."/> | 10 help="If empty, upload or import a SAM/BAM dataset."/> |