--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpcompletion.xml	Tue Mar 28 12:08:32 2023 +0000
@@ -0,0 +1,80 @@
+<tool id="rptools_rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+    <description>Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="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 '$adv.max_subpaths_filter'
+        --cache-dir "\${TMPDIR:-.}"
+    ]]></command>
+    <inputs>
+        <param name="rp2paths_pathways" type="data" format="csv" label="RP2paths pathways" />
+        <param name="rp2paths_compounds" type="data" format="tabular" label="RP2paths compounds" />
+        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
+        <param name="sink" type="data" format="csv" label="Sink from SBML" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." />
+            <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
+            <param argument="lower_flux_bound" type="integer" value="-10000" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="pathways" type="list" label="${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 outputs are represented in an expected number  -->
+            <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" count="9"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+rpCompletion
+============
+
+Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ 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:
+
+* **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file
+* **Sink from SBML**: rpextractsink file containing infos on molecules in the sink
+* **RP2paths compounds**: rp2paths compounds file
+* **RP2paths pathways**: rp2paths pathways file
+
+Advanced options:
+
+* **Upper flux bound**: (integer, default=9999) Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
+* **Lower flux bound**: (integer, default=0) Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
+* **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway.
+
+Output
+------
+
+* **pathways**: SBML completed pathways
+    ]]></help>
+    <expand macro="creator"/>
+    <citations>
+        <citation type="doi">10.1038/s41467-022-32661-x</citation>
+    </citations>
+</tool>