# HG changeset patch # User devteam # Date 1390523536 18000 # Node ID 3a18b0c7aa7d831057125dbd70d783c5ee6e015a # Parent 86e7e072c4c9f402753b6e4cf3149bd5f0704cc5 Uploaded diff -r 86e7e072c4c9 -r 3a18b0c7aa7d picard_CleanSam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CleanSam.xml Thu Jan 23 19:32:16 2014 -0500 @@ -0,0 +1,31 @@ +<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> + + <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