--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/selenzy.xml	Wed Dec 15 13:59:04 2021 +0000
@@ -0,0 +1,98 @@
+<tool id="selenzy-wrapper" name="Selenzyme" version="0.1.0">
+    <description>Performs enzyme selection from a reaction query</description>
+	<requirements>
+        <requirement type="package" version="0.1.0">selenzy_wrapper</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+	    python -m selenzy_wrapper '$pathway' '$uniprot_ids'
+        --nb_targets '$adv.nb_targets'
+        --d '$adv.direction'
+        #if str($adv.NoMSA) == "false":
+            --NoMSA
+        #end if
+        --taxonIDs '$adv.taxonIDs'
+        --nb_ids '$adv.nb_ids'
+        --to_csv '$uniprot_ids_csv'
+    ]]></command>
+    <inputs>
+		<param name="pathway" type="data" format="xml" label="Pathway (SBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+		    <param name="nb_ids"        type="integer" value="-1"       label="Number of uniprot IDs with top score to keep" />
+		    <param name="nb_targets"        type="integer" value="500"       label="Number of targets to display in results" />
+            <param name="direction"        type="float" value="0"       label="Use similiarity values for preferred reaction direction only" />
+            <param name="NoMSA"     type="boolean" label="Do not compute MSA/conservation scores ?"       checked="true"   display="checkboxes" />
+            <param name="taxonIDs" type="text" label="Comma separated taxon ids (first considered as the host)" value="83333" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="uniprot_ids" format="xml" label="Uniprot IDs" />
+        <data name="uniprot_ids_csv" format="csv" label="Uniprot IDs" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="pathway" value="pathway.xml" />
+            <output name="uniprot_ids" file="uniprod_ids_out.xml" ftype="xml" compare="diff" sort="true"/>
+            <output name="uniprot_ids_csv" file="uniprod_ids_out.csv" ftype="csv" compare="diff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Selenzyme
+================
+
+Performs enzyme selection from a reaction query.
+
+Input
+-----
+
+* **pathway_file**\ : (string) path to pathway file
+* **nb_targets**\ : (integer) Number of targets to display in results (before taxon IDs filtering) [default = 20]
+* **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
+* **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)]
+* **NoMSA**\ : (boolean) Do not compute MSA/conservation scores
+* **taxonIDs**\ : (string) Comma separated taxon ids [default: 83333 (E. coli K12)]. The first taxon ID is the one of the chassis, following ones are taxon IDs of output enzyme sequences
+
+Output
+------
+
+* **outfile**\ : (string) Path to output file
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/brsynth/selenzy-wrapper>`_
+
+Version
+----------
+
+0.1.0
+
+Authors
+-------
+* **Joan Hérisson**
+
+License
+-------
+
+* `MIT <https://github.com/brsynth/selenzy-wrapper/blob/master/LICENSE>`_
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@article{10.1093/bioinformatics/bty065,
+  title={Selenzyme: enzyme selection tool for pathway design},
+  author={Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J Turner, Nigel S Scrutton, Douglas B Kell, Rainer Breitling, Jean-Loup Faulon},
+  volume={34},
+  pages={2153–2154},
+  year={2018},
+  doi = {10.1093/bioinformatics/bty065},
+  url = {https://doi.org/10.1093/bioinformatics/bty065},
+}
+        </citation>
+    </citations>
+</tool>
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