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author | devteam |
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date | Wed, 19 Feb 2014 17:00:55 -0500 |
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<tool id="picard_cleansam" name="CleanSam" version="1.106.0"> <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CleanSam Read SAM and perform various fix-ups. Currently, the only fix-ups are 1: to soft-clip an alignment that hangs off the end of its reference sequence; and 2: to set MAPQ to 0 if a read is unmapped. --> <description>Read SAM and perform various fix-ups.</description> <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> <command interpreter="bash"> cleansamwrapper.sh $input1 $output1 </command> <inputs> <param name="input1" type="data" format="sam" label="SAM File to clean" /> </inputs> <outputs> <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}"> </data> </outputs> <tests> <test> <param name="input1" value="cleansamtestinput.sam" /> <output name="output1" file="cleansamtestoutput.sam" ftype="sam" /> </test> </tests> <help> **What it does** Read SAM and perform various fix-ups. Currently, the only fix-up it to soft-clip an alignment that hangs off the end of its reference sequence. </help> </tool>