Mercurial > repos > xuebing > bed_clean
view bedclean.xml @ 6:8fcf33cf58be
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author | xuebing |
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date | Sat, 31 Mar 2012 13:03:54 -0400 |
parents | 5807ee1f8653 |
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<tool id="bedclean" name="clean interval"> <description>remove off-chromosome lines</description> <command interpreter="python">bedclean.py $input $genome $output > $log </command> <inputs> <param name="input" type="data" format="interval" label="Original interval file"/> <param name="genome" type="select" label="Select chromsome size file" > <options from_file="chrsize.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> </inputs> <outputs> <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/> <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/> </outputs> <help> **Description** remove lines that are 1. comment or track name lines 2. on chr*_random 3. or have negative coordinates 4. or the end is larger than chromosome size </help> </tool>