diff find_in_reference.xml @ 1:856033fb26e8

Add case insensitive option

--- a/find_in_reference.xml	Sat Jan 04 09:03:57 2014 -0500
+++ b/find_in_reference.xml	Fri Jan 17 14:50:53 2014 -0600
@@ -7,6 +7,7 @@
     --input_column $column.input_column
     --reference_column $column.reference_column
   #end if
+  $case_insensitive
   #if 'novel' in $outputs.__str__ or not 'found' in $outputs.__str__:
     --output "$novel"
   #end if
@@ -16,9 +17,9 @@
   </command>
   <inputs>
     <param name="input" type="data" format="tabular" label="Input file to be filtered" 
-           help="e.g. tophat junctions.bed run without GTF option or no-novel-junctions"/> 
+           help="e.g. a peptide fasta converted to tabular"/> 
     <param name="reference" type="data" format="tabular" label="reference file to search" 
-           help="e.g. tophat junctions.bed run with GTF option and no-novel-junctions"/> 
+           help="e.g. a protein fasta converted to tabular"/> 
     <conditional name="column">
       <param name="set" type="select" label="select columns to compare">
         <option value="no" selected="true">Use last column of input and reference</option>
@@ -32,6 +33,7 @@
            help=""/>
       </when>
     </conditional>
+    <param name="case_insensitive" type="boolean" truevalue="--case_insensitive" falsevalue="" checked="false" label="Ignore case when comparing"/>
     <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>
@@ -58,11 +60,34 @@
   <help>
 **Find in Reference**
 
-Filters lines of a tabular input file by checking if the selected input column 
+Filters lines of a tabular input file by checking if the selected input column value
 is a substring of the selected column of any line in the reference file.  
 
 This can be used to check if peptides sequences are present in a set of reference proteins,  
 as a means of filtering out uninteresting peptide sequences.
 
+For Example with::
+
+  Input
+    >pep1	LIL
+    >pep2	WTF
+    >pep3	ISK
+
+  Reference
+    >prot1	RLET
+    >prot2	LLIL
+    >prot3	LAPSE
+    >prot3	RISKY
+
+  The outputs
+
+  Not found in reference
+    >pep2	WTF
+
+  Found in reference
+    >pep1	LIL
+    >pep3	ISK
+
+
   </help>
 </tool>