| Previous changeset 11:2da30502c2f1 (2013-03-14) Next changeset 13:03045debed6e (2013-04-17) |
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Commit message:
Updated CompareOverlappingSmallRef.xml |
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modified:
SMART/galaxy/CompareOverlappingSmallRef.xml |
| b |
| diff -r 2da30502c2f1 -r 5a054da77808 SMART/galaxy/CompareOverlappingSmallRef.xml --- a/SMART/galaxy/CompareOverlappingSmallRef.xml Thu Mar 14 05:37:08 2013 -0400 +++ b/SMART/galaxy/CompareOverlappingSmallRef.xml Thu Mar 14 05:37:35 2013 -0400 |
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| @@ -33,13 +33,24 @@ #if $OptionDistance.Dist == 'Yes': -d $OptionDistance.distance #end if - #if $OptionColinearOrAntiSens.OptionCA == 'Colinear': + #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 $OptionColinearOrAntiSens.OptionCA == 'AntiSens': + #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': -a #end if $InvertMatch $NotOverlapping + $OptionInclusionQuery + $OptionInclusionRef </command> <inputs> @@ -111,24 +122,56 @@ <when value="No"> </when> </conditional> - <conditional name="OptionColinearOrAntiSens"> - <param name="OptionCA" type="select" label="Colinear or anti-sens"> - <option value="Colinear">Colinear</option> + <conditional name="OptionMinOverlap"> + <param name="present" type="select" label="Minimum number of common nucleotides to declare an 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="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"> + <option value="Collinear">Collinear</option> <option value="AntiSens">AntiSens</option> <option value="NONE" selected="true">NONE</option> </param> - <when value="Colinear"> + <when value="Collinear"> </when> <when value="AntiSens"> </when> <when value="NONE"> </when> </conditional> - - <conditional name="OptionDistance"> <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."/> - </conditional> </inputs> <outputs> |