Mercurial > repos > devteam > picard1106
changeset 51:f53372fd8631 draft
Uploaded
| author | devteam |
|---|---|
| date | Mon, 17 Feb 2014 00:03:27 -0500 |
| parents | 1a2500b0df93 |
| children | e5b4ed9e0dbd |
| files | picard_CleanSam.xml |
| diffstat | 1 files changed, 36 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CleanSam.xml Mon Feb 17 00:03:27 2014 -0500 @@ -0,0 +1,36 @@ +<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> \ No newline at end of file