--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpcompletion.xml	Tue Nov 23 13:45:45 2021 +0000
@@ -0,0 +1,106 @@
+<tool id="rpCompletion" name="Complete Reactions" version="5.9.2">
+    <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description>
+    <requirements>
+        <requirement type="package" version="5.9.2">rptools</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1" level="fatal" description="Could not Xref compartment_id" />
+        <exit_code range="2" level="fatal" description="ValueError returned" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rptools.rpcompletion
+        '$rp2_pathways'
+        '$sink'
+        '$rp2paths_compounds'
+        '$rp2paths_pathways'
+        completed_pathways
+        --upper_flux_bound '$adv.upper_flux_bound'
+        --lower_flux_bound '$adv.lower_flux_bound'
+        --max_subpaths_filter '$adv.max_subpaths_filter'
+    ]]></command>
+    <inputs>
+        <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
+        <param name="rp2paths_compounds" type="data" format="tsv" label="RP2paths compounds" />
+        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
+        <param name="sink" type="data" format="csv" label="Sink from SBML" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" />
+            <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" />
+            <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" />
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="pathways" type="list" label="${tool.name}">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml" format="xml" directory="completed_pathways" visible="false" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="rp2paths_pathways" value="4-rp2paths_pathways.csv" />
+            <param name="rp2paths_compounds" value="3-rp2paths_compounds.tsv" />
+            <param name="rp2_pathways" value="1-rp2_metnet.csv" />
+            <param name="sink" value="2-sink.csv" />
+            <output_collection name="pathways" type="list">
+                <element name="rp_001_0001" ftype="xml" file="rp_001_0001.xml" sort="true"/>
+                <element name="rp_001_0006" ftype="xml" file="rp_001_0006.xml" sort="true"/>
+                <element name="rp_001_0011" ftype="xml" file="rp_001_0011.xml" sort="true"/>
+                <element name="rp_002_0001" ftype="xml" file="rp_002_0001.xml" sort="true"/>
+                <element name="rp_002_0011" ftype="xml" file="rp_002_0011.xml" sort="true"/>
+                <element name="rp_002_0021" ftype="xml" file="rp_002_0021.xml" sort="true"/>
+                <element name="rp_003_0001" ftype="xml" file="rp_003_0001.xml" sort="true"/>
+                <element name="rp_003_0131" ftype="xml" file="rp_003_0131.xml" sort="true"/>
+                <element name="rp_003_0261" ftype="xml" file="rp_003_0261.xml" sort="true"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+rpCompletion
+============
+
+Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
+
+Input
+-----
+
+Required:
+
+* **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file
+* **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink
+* **rp2paths_compounds**: (string) Path to the rp2paths compounds file
+* **rp2paths_pathways**: (string) Path to the rp2paths pathways file
+* **outdir**: (string) Path to the output directory containing sbml completed pathways
+
+Advanced options:
+
+* **-upper_flux_bound**: (integer, default=9999) Upper flux bound value
+* **-lower_flux_bound**: (integer, default=0) Lower flux bound value
+* **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path
+
+Project Links
+---------------------
+* `GitHub <https://github.com/brsynth/rptools>`_
+
+Version
+----------
+
+5.9.2
+
+Authors
+-------
+
+* **Melchior du Lac**
+* **Joan Hérisson**
+
+Acknowledgments
+---------------
+
+* Thomas Duigou
+
+Licence
+-------
+
+`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
+
+    ]]></help>
+</tool>
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