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SMART/galaxy/CompareOverlappingSmallQuery.xml |
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| diff -r 5a054da77808 -r 03045debed6e SMART/galaxy/CompareOverlappingSmallQuery.xml --- a/SMART/galaxy/CompareOverlappingSmallQuery.xml Thu Mar 14 05:37:35 2013 -0400 +++ b/SMART/galaxy/CompareOverlappingSmallQuery.xml Wed Apr 17 10:39:35 2013 -0400 |
| b |
| @@ -36,21 +36,13 @@ #if $OptionMinOverlap.present == 'Yes': -m $OptionMinOverlap.minOverlap #end if - #if $OptionPcOverlapQuery.present == 'Yes': - -p $OptionPcOverlapQuery.minOverlap - #end if - #if $OptionPcOverlapRef.present == 'Yes': - -P $OptionPcOverlapRef.minOverlap - #end if #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': -c - #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': + #elif $OptionCollinearOrAntiSens.OptionCA == 'Antisense': -a #end if $InvertMatch $NotOverlapping - $OptionInclusionQuery - $OptionInclusionRef </command> <inputs> @@ -112,7 +104,7 @@ </when> </conditional> <conditional name="OptionDistance"> - <param name="Dist" type="select" label="Maximum Distance between two reads"> + <param name="Dist" type="select" label="Maximum Distance between two regions"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> @@ -133,45 +125,21 @@ <when value="No"> </when> </conditional> - <conditional name="OptionPcOverlapQuery"> - <param name="present" type="select" label="N% of the query must overlap"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="minOverlap" type="integer" value="0"/> - </when> - <when value="No"> - </when> - </conditional> - <conditional name="OptionPcOverlapRef"> - <param name="present" type="select" label="N% of the reference must overlap"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="minOverlap" type="integer" value="0"/> - </when> - <when value="No"> - </when> - </conditional> - <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must nested in a query"/> - <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must nested in a query"/> <conditional name="OptionCollinearOrAntiSens"> - <param name="OptionCA" type="select" label="Collinear or anti-sens"> + <param name="OptionCA" type="select" label="Collinear or Antisense"> <option value="Collinear">Collinear</option> - <option value="AntiSens">AntiSens</option> + <option value="Antisense">Antisense</option> <option value="NONE" selected="true">NONE</option> </param> <when value="Collinear"> </when> - <when value="AntiSens"> + <when value="Antisense"> </when> <when value="NONE"> </when> </conditional> <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match"/> - <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by defalt."/> + <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="When there is no overlapping, the number of Overlapping will be set to 0 by default."/> </inputs> <outputs> |