Mercurial > repos > devteam > picard1106
comparison picard_CleanSam.xml @ 51:f53372fd8631 draft
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| author | devteam |
|---|---|
| date | Mon, 17 Feb 2014 00:03:27 -0500 |
| parents | 5b53bf15be53 |
| children |
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| 50:1a2500b0df93 | 51:f53372fd8631 |
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| 1 <tool id="picard_cleansam" name="CleanSam" version="1.106.0"> | |
| 2 <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CleanSam | |
| 3 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. | |
| 4 --> | |
| 5 <description>Read SAM and perform various fix-ups.</description> | |
| 6 | |
| 7 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> | |
| 8 | |
| 9 <command interpreter="bash"> | |
| 10 cleansamwrapper.sh $input1 $output1 | |
| 11 </command> | |
| 12 | |
| 13 <inputs> | |
| 14 <param name="input1" type="data" format="sam" label="SAM File to clean" /> | |
| 15 </inputs> | |
| 16 | |
| 17 <outputs> | |
| 18 <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}"> | |
| 19 </data> | |
| 20 </outputs> | |
| 21 | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="input1" value="cleansamtestinput.sam" /> | |
| 25 <output name="output1" file="cleansamtestoutput.sam" ftype="sam" /> | |
| 26 </test> | |
| 27 </tests> | |
| 28 | |
| 29 <help> | |
| 30 | |
| 31 **What it does** | |
| 32 | |
| 33 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. | |
| 34 | |
| 35 </help> | |
| 36 </tool> |