--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getgo.xml	Sun Feb 28 11:52:10 2016 -0500
@@ -0,0 +1,43 @@
+<tool id="getgo" name="Retrieve GO ontologies" version="0.1.0">
+    <description />
+    <requirements>
+        <requirement type="package" version="3.2.1">R</requirement>
+        <requirement type="package" version="1.22.0">goseq</requirement>
+    </requirements>
+    <command interpreter="Rscript">
+        getgo.r --genome "$genome"
+        --gtf "$gtf"
+        --gene_id "$gene_id"
+        --output "$output"
+        --cats "$cats"
+    </command>
+    <inputs>
+        <param name="gtf" label="select GTF file" help="GO annotations for all gene ids in this GTF will be fetched" type="data" format="gtf"/>
+        <param help="Needed to retrieve GO annotations for the selected genome" label="Select the genome source" name="genome" size="3" type="select">
+            <options from_data_table="go_genomes"></options>
+        </param>
+        <param help="Needed for GO analysis" label="Select gene identifier format" name="gene_id" type="select">
+            <options from_data_table="go_gene_ids"></options>
+        </param>
+        <param name="cats" help="Select the categories for which you would like to retrieve ontologies" type="select" multiple="true" display="checkboxes">
+            <option value="GO:CC">GO:Cellular Components</option>
+            <option value="GO:BP">BiologicalProcesses</option>
+            <option value="GO:MF">Molecular Function</option>
+            <option value="KEGG">KEGG pathway</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="tabular" label="GO category mapping" name="output" />
+    </outputs>
+    <tests></tests>
+    <help>
+
+        **What it does**
+
+        Returns a tabular file with GO gene categories.
+
+
+        </help>
+    <citations>
+    </citations>
+</tool>