--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnacommender.xml	Thu Jul 28 05:56:54 2016 -0400
@@ -0,0 +1,48 @@
+<tool id="rbc_rnacommender" name="RNAcommender" version="0.1.1">
+    <description>genome-wide recommendation of RNA-protein interactions</description>
+    <requirements>
+        <requirement type="package" version="3.5">sam</requirement>
+        <requirement type="package" version="1.11.1">numpy</requirement>
+        <requirement type="package" version="0.17.1">scipy</requirement>
+        <requirement type="package" version="0.18.1">pandas</requirement>
+        <requirement type="package" version="3.2.2">pytables</requirement>
+        <requirement type="package" version="0.8.2">theano</requirement>
+        <requirement type="package" version="2.10.0">requests</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+    <![CDATA[
+        sh $__tool_directory__/init.sh 2> hide.txt &&
+        THEANO_FLAGS=base_compiledir=./tmp python $__tool_directory__/main.py "$infile"
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="fasta" label="Fasta file containing (exactly) one RBP sequence"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" from_work_dir="output.txt" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="sample.fa" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_text_matching expression="RBP\ttarget\ty_hat"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        RNAcommender 0.1.0 (GALAXY version).
+        In order to get the prediction for one (or more) RBPs, insert one fasta file with the protein sequences. The output will contain a ranked list of targets for ALL the proteins in the input file.
+        RNAcommender full package is available at https://github.com/gianlucacorrado/RNAcommender.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @ARTICLE{corrado2016rnacommender,
+                Author = {Gianluca Corrado, Toma Tebaldi, Fabrizio Costa, Paolo Frasconi and Andrea Passerini},
+                keywords = {machine learning, bioinformatics, post-trainscriptional regulation, gene expression},
+                title = {{RNAcommender: genome-wide recommendation of RNA-protein interactions.}},
+                url = {https://github.com/gianlucacorrado/RNAcommender}
+            }
+        </citation>
+    </citations>
+</tool>