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comparison rgPicardMarkDups.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
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1:e0232cbac965 2:9227b8c3093b
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."/>