--- a/rpcompletion.xml	Tue Mar 28 12:05:15 2023 +0000
+++ b/rpcompletion.xml	Fri Oct 24 08:37:01 2025 +0000
@@ -1,80 +1,115 @@
-<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>
+<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"/>
+    <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" />
+        <regex match="Continuing without sink molecule" source="both" level="warning"
+            description="The sink file is empty or not found" />
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
+        TMPDIR="\${TMPDIR:-.}/rr_cache" &&
+        mkdir -p "\${TMPDIR}" &&
+        #if str($sink.cond) == 'empty'
+            echo '"Name","InChI"' > empty_sink.csv &&
+            #set sinkfile='empty_sink.csv'
+        #else
+            #set sinkfile=$sink.sinkfile
+        #end if
+
         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 '$adv.max_subpaths_filter'
-        --cache-dir "\${TMPDIR:-.}"
+            '$rp2_pathways'
+            $sinkfile
+            '$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'
+            --chemical-space '$adv.chemical_space'
+            #if $adv.cofile
+                --cofactors '$adv.cofile'
+            #end if
+            #if not $sink.error_codes
+                --silent
+            #end if
+            --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" />
+        <conditional name="sink">
+            <param name="cond" type="select" label="Empty sink">
+                <option value="provided" selected="True">Provided</option>
+                <option value="empty">Empty</option>
+            </param>
+            <when value="provided">
+                <param name="sinkfile" type="data" format="csv" label="Sink File"
+                    help="Sink file which comprises all compounds that are considered as granted in your system." />
+                <param name="error_codes" type="boolean" checked="true"
+                    label="Return error codes" />
+            </when>
+            <when value="empty">
+                <param name="error_codes" type="boolean" checked="false"
+                    label="Return error codes" />
+            </when>
+        </conditional>
         <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." />
+            <param argument="max_subpaths_filter" type="integer" value="10" min="0"
+                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." />
+            <param name="chemical_space" type="select" label="Chemical space">
+                <option value="mnx4.4" selected="True">mnx4.4</option>
+                <option value="mnx3.1">mnx3.1</option>
+            </param>
+            <param name="cofile" type="data" format="txt,tsv,tabular" optional="True"
+                label="Cofactor file" />
         </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" />
+            <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  -->
+            <!-- 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"/>
+            <conditional name="sink">
+                <param name="cond" value="provided" />
+                <param name="sinkfile" value="2-sink.csv" />
+            </conditional>
+            <output_collection name="pathways" type="list" count="10" />
         </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.
+Completes mono-component reactions output by `RetroPath2.0 <https://www.doi.org/10.1016/j.ymben.2017.12.002>`_ 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.
 
 Output
 ------
 
 * **pathways**: SBML completed pathways
     ]]></help>
-    <expand macro="creator"/>
+    <expand macro="creator" />
     <citations>
         <citation type="doi">10.1038/s41467-022-32661-x</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file