# HG changeset patch
# User tduigou
# Date 1759745305 0
# Node ID 5ff2b0c02dd61d22eec412609e4a8b6b32aadf7d
# Parent  4462f4c997ba9d394680bddbddc9d846e47cce54
planemo upload for repository https://github.com/brsynth/rp2paths commit 41f01844826821a31f79851a6bc9106c5378b7c5-dirty

diff -r 4462f4c997ba -r 5ff2b0c02dd6 rp2paths.xml
--- a/rp2paths.xml	Fri Oct 03 12:18:46 2025 +0000
+++ b/rp2paths.xml	Mon Oct 06 10:08:25 2025 +0000
@@ -1,6 +1,8 @@
-<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09" license="MIT">
+<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"
+    license="MIT">
     <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
     <macros>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@TOOL_VERSION@">2.1.0</token>
     </macros>
     <requirements>
@@ -13,29 +15,29 @@
     </stdio>
     <command detect_errors="exit_code"><![CDATA[
         mkdir out &&
-        python -m rp2paths all
+        python -m rp2paths --no-color all
         '$rp2_pathways'
         --outdir out
-        --timeout '$adv.timeout' 
-        #if str($adv.forward) == 'true'
+        #if str($general.forward) == 'true'
             --forward
         #end if
-        #if $adv.cofile
-            --cofile '$adv.cofile'
+        #if $cofactor_removal.cofile
+            --cofile '$cofactor_removal.cofile'
         #end if
-        #if str($adv.mindepth) == 'true'
+        #if str($scope.mindepth) == 'true'
             --minDepth
         #end if
-        #if $adv.sink
-            --customsinkfile '$adv.sink'
+        #if $scope.sink
+            --customsinkfile '$scope.sink'
         #end if
-        --maxsteps '$adv.maxsteps'
-        --maxpaths '$adv.maxpaths'
-        #if str($adv.unfold) == 'true'
+        --timeout '$path_enum.timeout'
+        --maxsteps '$path_enum.maxsteps'
+        --maxpaths '$path_enum.maxpaths'
+        #if str($path_enum.unfold) == 'true'
             --unfold_compounds
         #end if
         #set cmp_ids = []
-        #for $x in $adv.rep_include_path
+        #for $x in $path_enum.rep_include_path
             #silent cmp_ids.append(str($x.cmp_id))
         #end for
         #if len(cmp_ids) > 0
@@ -43,17 +45,14 @@
             --onlyPathsStartingBy $cmp_id
         #end if
         #set cmp_ids = []
-        #for $x in $adv.rep_exclude_path
+        #for $x in $path_enum.rep_exclude_path
             #silent cmp_ids.append(str($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 '$adv.target' &&
+        --target '$dev.target' &&
         mv out/compounds.txt out/compounds.tsv &&
         cp out/compounds.tsv '$compounds' &&
         if test -f 'out/out_paths.csv'; then
@@ -63,20 +62,27 @@
     <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." />
-        <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." />
+        <section name="general" title="General" expanded="false">
             <param
                 name="forward" type="boolean" checked="false" label="Forward"
                 help="Consider reactions in the forward direction" />
+        </section>
+        <section name="cofactor_removal" title="Cofactor removal" expanded="False">
             <param name="cofile"
                 type="data" format="csv" optional="True" label="List of cofactors" />
+        </section>
+        <section name="scope" title="Scope" expanded="False">
             <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" />
+                name="mindepth" type="boolean" checked="false" label="Minimal Depth Scope Only"
+                help="Use minimal depth scope only, 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"
+                name="sink" type="data" format="tabular" optional="True"
+                label="List of custom sinks"
                 help="Listing compounds to consider as sink compounds. Sink compounds should be provided by their IDs, as used in the reaction.erxn file" />
+        </section>
+        <section name="path_enum" title="Pathways enumeration" 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="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" />
@@ -86,23 +92,25 @@
             <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"
+            <repeat name="rep_include_path" title="Only include pathways starting by compounds.."
+                help="List of compounds IDs to consider. If specified, only pathways making use of at least one of these compounds as initial substrate (first step of a pathway) will be returned. Leave empty to keep all.">
+                <param name="cmp_id" type="text" label="Pathway 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">
+            <repeat name="rep_exclude_path" title="Exclude pathways starting by compounds.."
+                help="List of compounds IDs to exclude. If specifed, pathways making use of any of these compounds as unique initial substrate will be filtered out. Leave empty for no exclusion.">
                 <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" />
+        </section>
+        <section name="dev" title="Dev" expanded="false">
             <param
                 name="target" type="text" value="TARGET_0000000001"
-                label="Target compound internal ID"
+                label="Target compound internal ID (Internal)"
                 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>