# HG changeset patch
# User jfallmann
# Date 1485960855 18000
# Node ID 52d2bcae95e27fe5d9608d68edb2184d8989cbf2

Uploaded xml

diff -r 000000000000 -r 52d2bcae95e2 aresite2.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/aresite2.xml	Wed Feb 01 09:54:15 2017 -0500
@@ -0,0 +1,53 @@
+<tool id="AREsite2_REST" name="Get motifs from AREsite2" version="0.1.2">
+    <description>AREsite2 REST Interface</description>
+    <requirements>
+        <requirement type="package" version="2.12.4">requests</requirement>
+        <requirement type="package" version="1.10.0">six</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+python $__tool_directory__/aresite2.py
+-g $gene
+-m "$motif"
+-s $species_selector
+> $AREsite2_REST_out
+]]>
+    </command>
+
+    <inputs>
+    <param name="gene" type="text" label="Gene ID to search for" help="Try e.g. cxcl2" />
+    <param name="species_selector" type="select" label="Select species">
+        <option value="Homo_sapiens" selected="true"></option>
+        <option value="Mus_musculus"></option>
+	<option value="Danio_rerio"></option>
+	<option value="Drosophila_melanogaster"></option>
+	<option value="Caenorhabditis_elegans"></option>
+    </param>
+    <param name="motif" type="text" label="Motif to search for" help="Choose a single motif, e.g. ATTTA" />
+    </inputs>
+
+    <outputs>
+        <data name="AREsite2_REST_out" label="AREsite2_Rest_${motif}_${gene}_${species_selector}" type="text" format="bed" />
+    </outputs>
+
+    <tests>
+        <test>
+          <param name="species" value="Homo_sapiens" />
+          <param name="motif" value="ATTTA" />
+	  <param name="gene" value="Cxcl2" />
+          <output name="outputFile" file="AREsite2_Rest_ATTTA_cxcl2_Homo_sapiens.bed" />
+        </test>
+    </tests>
+
+    <help>
+<![CDATA[
+**What it does**
+
+Retrieve motif information in BED format from AREsite2 using its REST API.
+
+]]>
+    </help>
+    <citations>
+      <citation type="doi">10.1093/nar/gkv1238</citation>
+    </citations>
+</tool>