# HG changeset patch
# User tduigou
# Date 1759493926 0
# Node ID 4462f4c997ba9d394680bddbddc9d846e47cce54
# Parent  016ae4a7705edf7be2f668a1d4dd14f372e7d4e4
planemo upload for repository https://github.com/brsynth/rp2paths commit 1a817217fcd199ae61266ec6133137a87f4ab4be-dirty

diff -r 016ae4a7705e -r 4462f4c997ba rp2paths.xml
--- a/rp2paths.xml	Wed Jul 24 08:42:00 2024 +0000
+++ b/rp2paths.xml	Fri Oct 03 12:18:46 2025 +0000
@@ -1,14 +1,14 @@
 <tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
     <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.5.1</token>
+        <token name="@TOOL_VERSION@">2.1.0</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
     </requirements>
     <stdio>
         <regex match="TIMEOUT:" level="fatal" />
-        <regex match="ERROR:"   level="fatal" />
+        <regex match="ERROR:" level="fatal" />
         <regex match="WARNING:" level="warning" />
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
@@ -16,7 +16,44 @@
         python -m rp2paths all
         '$rp2_pathways'
         --outdir out
-        --timeout '$adv.timeout' &&
+        --timeout '$adv.timeout' 
+        #if str($adv.forward) == 'true'
+            --forward
+        #end if
+        #if $adv.cofile
+            --cofile '$adv.cofile'
+        #end if
+        #if str($adv.mindepth) == 'true'
+            --minDepth
+        #end if
+        #if $adv.sink
+            --customsinkfile '$adv.sink'
+        #end if
+        --maxsteps '$adv.maxsteps'
+        --maxpaths '$adv.maxpaths'
+        #if str($adv.unfold) == 'true'
+            --unfold_compounds
+        #end if
+        #set cmp_ids = []
+        #for $x in $adv.rep_include_path
+            #silent cmp_ids.append(str($x.cmp_id))
+        #end for
+        #if len(cmp_ids) > 0
+            #set cmp_id = ' '.join($cmp_ids)
+            --onlyPathsStartingBy $cmp_id
+        #end if
+        #set cmp_ids = []
+        #for $x in $adv.rep_exclude_path
+            #silent cmp_ids.append(str($x.cmp_id))
+        #end for
+        #if len(cmp_ids) > 0
+            #set cmp_id = ' '.join($cmp_ids)
+            --notPathsStartingBy $cmp_id
+        #end if 
+        #if $adv.cmpfile
+            --cmpdnamefile '$adv.cmpfile'
+        #end if
+        --target '$adv.target' &&
         mv out/compounds.txt out/compounds.tsv &&
         cp out/compounds.tsv '$compounds' &&
         if test -f 'out/out_paths.csv'; then
@@ -24,21 +61,63 @@
         fi
     ]]></command>
     <inputs>
-        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/>
+        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways"
+            help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis." />
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />
+            <param name="timeout" type="integer" value="1800" label="Time Out"
+                help="Time out before killing a process (in seconds), default: 30 minutes." />
+            <param
+                name="forward" type="boolean" checked="false" label="Forward"
+                help="Consider reactions in the forward direction" />
+            <param name="cofile"
+                type="data" format="csv" optional="True" label="List of cofactors" />
+            <param
+                name="mindepth" type="boolean" checked="false" label="Minimal depth scope"
+                help="Use minimal depth scope, i.e. stop the scope computation as as soon an a first minimal path linking target to sink is found" />
+            <param
+                name="sink" type="data" format="tabular" optional="True" label="List of sinks"
+                help="Listing compounds to consider as sink compounds. Sink compounds should be provided by their IDs, as used in the reaction.erxn file" />
+            <param
+                name="maxsteps" type="integer" min="0" value="0" max="20" label="Max steps"
+                help="Cutoff on the maximum number of steps in a pathways. 0 (default) for unlimited number of steps" />
+            <param
+                name="maxpaths" type="integer" min="0" value="0" max="20" label="Max pathways"
+                help="Cutoff on the maximum number of pathways. 0 (default) for unlimited number of pathways" />
+            <param
+                name="unfold" type="boolean" checked="false" label="Unfold pathways"
+                help="Unfold pathways based on equivalencie of compounds (can lead to combinatorial explosion)." />
+            <repeat name="rep_include_path" title="Include path starting by">
+                <param name="cmp_id" type="text" label="Path label"
+                    help="List of compounds IDs to consider. If specified, only paths making use of at least one of these compounds as initial substrate (first step of a pathway) are kept.">
+                    <validator type="empty_field" message="Not empty" />
+                </param>
+            </repeat>
+            <repeat name="rep_exclude_path" title="Include path starting by">
+                <param name="cmp_id" type="text" label="Path label"
+                    help="List of compounds IDs. If specifed, paths making use of one of these compounds as unique initial substrate will be filtered out">
+                    <validator type="empty_field" message="Not empty" />
+                </param>
+            </repeat>
+            <param name="cmpfile" type="data" format="tabular"
+                optional="True" label="List of compounds" help="File with name of compounds" />
+            <param
+                name="target" type="text" value="TARGET_0000000001"
+                label="Target compound internal ID"
+                help="This internal ID specifies which compound should be considered as the targeted compound. The default behavior is to consider as the target the first compound used as a source compound in a first iteration of a metabolic exploration. Let this value as it is except if you know what you are doing" />
         </section>
     </inputs>
     <outputs>
-        <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
-        <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
+        <data name="master_pathways" format="csv"
+            label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
+        <data name="compounds" format="tabular"
+            label="${tool.name} on ${rp2_pathways.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="tabular" compare="diff"/>
+            <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff" />
+            <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff" />
         </test>
     </tests>
     <help><![CDATA[
@@ -55,17 +134,6 @@
 
 |
 
-Input
------
-
-Required information:
-
-* **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.
-
-Advanced options:
-
-* **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
-
 Output
 ------
 
@@ -73,9 +141,9 @@
 * **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
     ]]></help>
     <creator>
-        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+        <organization name="BioRetroSynth" url="https://github.com/brsynth" />
     </creator>
     <citations>
         <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
     </citations>
-</tool>
+</tool>
\ No newline at end of file