Mercurial > repos > boris > filter_on_md
changeset 23:db73de0bc05b draft default tip
Updated config tool xml -- Fixes tool shed visualization issue
| author | boris |
|---|---|
| date | Tue, 24 Apr 2012 11:45:04 -0400 |
| parents | 20e1957ed95a |
| children | |
| files | MDtag_filter.xml |
| diffstat | 1 files changed, 4 insertions(+), 15 deletions(-) [+] |
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--- a/MDtag_filter.xml Fri Apr 20 16:36:41 2012 -0400 +++ b/MDtag_filter.xml Tue Apr 24 11:45:04 2012 -0400 @@ -1,27 +1,16 @@ <tool id="MDtag_filter" name="Filter mapped reads" version="1.0.2"> <description>on MD tag string</description> - <command interpreter="python">MDtag_filter.py $in_sam $n $m $out_sam ${create.choice} $discarded_sam</command> + <command interpreter="python">MDtag_filter.py $in_sam $n $m $out_sam $saveDiscarded $discarded_sam</command> <inputs> <param format="sam" name="in_sam" type="data" label="Input SAM file"/> <param name="n" type="integer" value='0' label="5' end window (n)" help="Any number of mismatches within this window will cause the read to be discarded"/> <param name="m" type="integer" value='0' label="3' end window (m)" help="Any number of mismatches within this window will cause the read to be discarded"/> - <conditional name="create"> - <param name="choice" type="select" label="Create additional SAM file for discarded reads?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"> - <!-- do nothing here --> - </when> - <when value="yes"> - <!-- do nothing here --> - </when> - </conditional> + <param name="saveDiscarded" label="Save discarded reads in additional SAM file?" type="boolean" truevalue="yes" falsevalue="no" checked="False"/> </inputs> <outputs> <data format="sam" name="out_sam" label="MDtag_filter_(selected)_from_${in_sam.name}" metadata_source="in_sam"/> <data format="sam" name="discarded_sam" label="MDtag_filter_(discarded)_from_${in_sam.name}" metadata_source="in_sam"> - <filter> (create['choice']=='yes') </filter> + <filter> saveDiscarded is True </filter> </data> </outputs> <tests> @@ -35,7 +24,7 @@ <param name="in_sam" value="test_for_md_filter.sam"/> <param name="n" value="5"/> <param name="m" value="5"/> - <param name="choice" value="yes"/> + <param name="saveDiscarded" value="yes"/> <output name="out_sam" file="test_md_selected.sam"/> <output name="discarded_sam" file="test_md_discarded.sam"/> </test>