--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_sequences.xml	Mon Dec 12 07:47:42 2016 -0500
@@ -0,0 +1,61 @@
+<tool id="get_sequences" name="Get sequences by Ensembl ID" version="0.1.1">
+    <description>using REST API</description>
+    <requirements>
+        <requirement type="package" version="2.7">requests</requirement>
+    </requirements>
+    <command>
+<![CDATA[
+python $__tool_directory__/get_sequences.py
+-s $species_selector
+--expand_3prime $expand_3prime
+--expand_5prime $expand_5prime
+-t $type_selector
+-i "$input"
+> "$output"
+]]>
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="txt" label="List of Ensembl IDs" />
+        <param name="species_selector" type="select" label="Select Species">
+            <option value="ensembl" selected="true">Vertebrates</option>
+            <option value="ensemblgenomes">Other species</option>
+        </param>
+        <param name="expand_3prime" type="integer" value="0" min="0" label="expand_3prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
+        <param name="expand_5prime" type="integer" value="0" min="0" label="expand_5prime" help="Expand each sequence downstream of the sequence by this many basepairs. Only available when using genomic sequence type." />
+        <param name="type_selector" type="select" label="Type" help="Type of sequence. Defaults to genomic where applicable, i.e. not translations. cDNA refers to the spliced transcript sequence with UTR; CDS refers to the spliced transcript sequence without UTR">
+            <option value="genomic" selected="true">Genomic</option>
+            <option value="cds">CDS</option>
+            <option value="cdna">cDNA</option>
+            <option value="protein">Protein</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="fasta" label="$(tool.name) on ${on_string}" />
+    </outputs>
+
+    <tests>
+          <test>
+                <param name="input" ftype="txt" value="input.txt" />
+                <param name="expand_3prime" value="0" />
+                <param name="expand_5prime" value="0" />
+                <param name="type_selector" value="genomic" />
+                <output name="output" file="sequences.fasta" />
+          </test>
+     </tests>
+
+    <help>
+<![CDATA[
+**What it does**
+
+Retrieves FASTA sequences from Ensembl using its REST API.
+
+Uses the `"POST sequence/id"`_ API endpoint.
+
+.. _"POST sequence/id": http://rest.ensembl.org/documentation/info/sequence_id_post
+]]>
+    </help>
+    <citations>
+    </citations>
+</tool>