# HG changeset patch
# User bgruening
# Date 1426846890 14400
# Node ID 97ecd7154f6b6c0ed956bceb7098a40d5ed8de81
# Parent  424b0639008438aec051f763879283c09b881299
Uploaded

diff -r 424b06390084 -r 97ecd7154f6b find_subsequences.xml
--- a/find_subsequences.xml	Fri Mar 20 06:05:15 2015 -0400
+++ b/find_subsequences.xml	Fri Mar 20 06:21:30 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="bg_find_subsequences" name="Subsequence search" version="0.1">
+<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.1">
     <description>providing regions in BED format</description>
     <requirements>
         <requirement type="package" version="1.65">biopython</requirement>
@@ -17,7 +17,7 @@
     ]]>
     </command>
     <inputs>
-        <param format="fasta,fastq" name="input" type="data" label="Sequence to be searched"
+        <param format="fasta,fastq" name="input" type="data" label="Nucleotide sequence to be searched"
             help="This can be in FASTA or FASTQ format." />
 
         <conditional name="pattern_conditional">
@@ -248,11 +248,6 @@
                 </param>
             </when>
         </conditional>
-
-
-
-          
-
     </inputs>
     <outputs>
         <data format="bed" name="output" />
@@ -282,10 +277,9 @@
 
 **What it does**
 
-Searches for a subsequence in a larger sequence. For example to get all restriction enzymes for BamHI.
+Searches for a subsequence in a larger nucleotide sequence. For example to get all restriction enzymes for BamHI.
 
-If you are searching in a DNA sequence you can use ambiguous values using the standard 
-`nucleotide ambiguity code <http://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html>`_.
+You can use ambiguous values using the standard `nucleotide ambiguity code <http://www.dnabaser.com/articles/IUPAC%20ambiguity%20codes.html>`_.
 
 This tool is searching on both strands.