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+<tool id="rp2paths" name="RP2paths" version="1.4.3">
+    <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
+    <requirements>
+        <requirement type="package" version="1.4.3">rp2paths</requirement>
+    </requirements>
+	<stdio>
+        <regex match="TIMEOUT:" level="fatal" />
+        <regex match="ERROR:"   level="fatal" />
+		<regex match="WARNING:" level="warning" />
+	</stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        #from os import path as os_path
+        cd /tmp &&
+        #set outFolder = os_path.basename(str($master_pathways))
+        mkdir '$outFolder' &&
+        python -m rp2paths all
+        '$rp2_pathways'
+        --outdir '$outFolder'
+        --timeout '$adv.timeout' &&
+        cp '$outFolder'/compounds.txt '$compounds' &&
+        cp '$outFolder'/out_paths.csv '$master_pathways' &&
+        rm -rf $outFolder
+    ]]></command>
+    <inputs>
+        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" />
+        <section name="adv" title="Advanced Options" expanded="false">
+			<param name="timeout" type="integer" value="1800" label="Time Out" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="master_pathways" format="csv" label="${tool.name} (Pathways)" />
+        <data name="compounds" format="tsv" label="${tool.name} (Compounds)" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="rp2_pathways" value="retropath2_pathways.csv" />
+            <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
+            <output name="compounds" file="rp2paths_compounds.tsv" ftype="tsv" compare="diff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+rp2paths
+========
+
+
+RP2paths extracts the set of pathways that lies in a metabolic space file output by the RetroPath2.0 workflow. Source code may be found at the following location: `GitHub <https://github.com/brsynth/rp2paths>`_.
+
+Input
+-----
+
+Required information:
+
+
+* **rp_results**\ : (string) Path to the ReatroPath2.0 pathways file
+
+Advanced options:
+
+
+* **timeout**\ : (string, default: 30 minutes) Time out time of the tool
+* **server_url**\ : (string) IP address of the rp2paths REST service
+
+Output
+------
+
+
+* **out_paths**\ : (string) Path to the RP2paths pathways. Describes all the indiviudal enumerated pathways that produce the compound of interest.
+* **out_compounds**\ : (string) Path to the RP2paths Compounds. Describes the structure of all the chemical species involved in all pathways.
+
+Versioning
+----------
+
+v1.4.3
+
+Authors
+-------
+
+
+* **Melchior du Lac**
+* Thomas Duigou
+* Baudoin Delépine
+* Pablo Carbonell
+
+License
+-------
+
+`MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_
+
+Acknowledgments
+---------------
+
+
+* Joan Hérisson
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@article{delepine2018retropath2,
+  title={RetroPath2.0: a retrosynthesis workflow for metabolic engineers},
+  author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
+  journal={Metabolic engineering},
+  volume={45},
+  pages={158--170},
+  year={2018},
+  publisher={Elsevier}}
+        </citation>
+    </citations>
+</tool>
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