--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/utils_find-boxes.xml	Thu Jul 28 10:25:37 2016 -0400
@@ -0,0 +1,90 @@
+<tool id="smf_utils_find-boxes" name="find-boxes" version="@VERSION@-1">
+    <description>Finds all occurances of two given boxes (sequence motifs) within a FASTA file</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <requirements>
+        <requirement type="package" version="2.7.10">python</requirement>
+        <requirement type="package" version="1.9">numpy</requirement>
+        <requirement type="package" version="0.8.2.1">pysam</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
+        <requirement type="package" version="2.0.1">segmentation-fold-utils</requirement>
+    </requirements>
+    
+    <expand macro="stdio" />
+
+    <version_command>@VERSION_COMMAND_UTILS@</version_command>
+    
+    <command><![CDATA[
+        segmentation-fold-utils
+            find-boxes
+                --box1 '${box1}'
+                --box2 '${box2}'
+                $forward
+                $reverse
+                '${fasta_input}'
+                '${bed_output}'
+    ]]></command>
+
+    <inputs>
+        <param name="fasta_input"
+               type="data"
+               format="fasta"
+               argument="-f"
+               label="Fasta file with RNA-sequece" />
+
+        <param name="box1"
+               type="text"
+               value="NRUGAUG"
+               argument="--box1"
+               label="Sequence of box1 (default = C-box: 'NRUGAUG')"
+               help="Sequence encoding can be found at the following url: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representations" />
+
+        <param name="box2"
+               type="text"
+               value="CUGA"
+               argument="--box2"
+               label="Sequence of box2 (default = D-box: 'CUGA')"
+               help="Sequence encoding can be found at the following url: https://en.wikipedia.org/wiki/FASTA_format#Sequence_representations" />
+
+        <param name="forward"
+               type="boolean"
+               truevalue="--forward"
+               falsevalue="--no-forward"
+               checked="true"
+               label="Search in the forward direction of the reference sequence" />
+
+        <param name="reverse"
+               type="boolean"
+               truevalue="--reverse"
+               falsevalue="--no-reverse"
+               checked="true"
+               label="Search in the reverse complement of the reference sequence" />
+    </inputs>
+
+    <outputs>
+        <data format="bed"
+              name="bed_output"
+              label="${tool.name} on ${str($fasta_input.hid) + ': ' + $fasta_input.name}" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="fasta_input" value="FindBoxes.genome.fa" format="fasta" />
+            <param name="box1" value="NRUGAUG" />
+            <param name="box2" value="CUGA" />
+            <param name="forward" value="--forward" />
+            <param name="reverse" value="--reverse" />
+            
+            <output name="bed_output" file="FindBoxes.test_02.bed" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Scans a FASTA reference for BOX motifs (like C- and D-box) and reports them in a BED file
+    ]]></help>
+    
+    <expand macro="citations" />
+</tool>