diff find_in_reference.xml @ 2:c4fd2ea4f988

Add the option to test the reversed sequence and the DNA reverse complement of the sequence (ignored if the sequence cannot be interpreted as DNA)

--- a/find_in_reference.xml	Wed Aug 13 15:01:33 2014 -0500
+++ b/find_in_reference.xml	Thu Nov 13 14:09:50 2014 -0600
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="find_in_reference" name="find in reference" version="0.0.2">
+<tool id="find_in_reference" name="find in reference" version="0.0.3">
   <description>filter peptides that are present in proteins</description>
   <command interpreter="python">find_in_reference.py  --input "$input" 
   --reference "$reference" 
@@ -7,7 +7,7 @@
     --input_column $column.input_column
     --reference_column $column.reference_column
   #end if
-  $case_insensitive $reverse_find
+  $case_insensitive $reverse_find $test_reverse $test_dna_reverse_complement
   #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
     --output "$novel"
   #end if
@@ -44,6 +44,8 @@
     </conditional>
     <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
     <param name="reverse_find" type="boolean" truevalue="--reverse_find" falsevalue="" checked="false" label="reverse search: find the reference in the input" />
+    <param name="test_reverse" type="boolean" truevalue="--test_reverse" falsevalue="" checked="false" label="Also search for reversed input string in the reference" />
+    <param name="test_dna_reverse_complement" type="boolean" truevalue="--test_dna_reverse_complement" falsevalue="" checked="false" label="Also search for the DNA reverse complementof of the input in the reference" />
     <param name="outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
       <option value="novel" selected="true">lines with no match in reference</option>
       <option value="found">lines with match in reference</option>