--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_subsequences.xml	Thu Mar 19 09:40:43 2015 -0400
@@ -0,0 +1,58 @@
+<tool id="bg_find_subsequences" name="Subsequence search" version="0.1">
+    <description>providing regions in BED format</description>
+    <requirements>
+        <requirement type="package" version="1.6.5">biopyhon</requirement>
+    </requirements>
+    <command interpreter="python">
+    <![CDATA[
+        find_subsequences.py
+            --input $input
+            --output $output
+            --pattern "$pattern"
+            #if $input.ext == 'fasta':
+                --format 'fasta'
+            #else:
+                --format 'fastq'
+            #end if
+    ]]>
+    </command>
+    <inputs>
+        <param format="fasta,fastq" name="input" type="data" label="Sequence to be searched"
+            help="This can be in FASTA or FASTQ format." />
+        <param name="pattern" type="text" value="" label="Search pattern" help="For example GGATCC for BamH1.">
+            <validator type="regex" message="Only letters are allowed.">^[a-zA-Z]+$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="bed" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/>
+            <param name="pattern" value="atcg"/>
+            <output name="output" file="find_subsequences_simple_result1.bed" ftype="bed"/>
+        </test>
+        <test>
+            <param name="input" value="find_subsequences_input1.fasta" ftype="fasta"/>
+            <param name="pattern" value="atnncg"/>
+            <output name="output" file="find_subsequences_advanced_result1.bed" ftype="bed"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+Searches for a subsequence in a larger sequence. For example to get all restriction enzymes for BamH1.
+
+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>`_.
+
+This tool is searching on both strands.
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
+</tool>