Mercurial > repos > metexplore > met4j_sbml2carbonskeletonnet

changeset 2:6c12298b1f5f draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit 71335d4a636672d264cc4f443c07856907571928
author metexplore
date Fri, 21 Nov 2025 10:22:17 +0000
parents 0317b47b4f11
children
files Sbml2CarbonSkeletonNet.xml macros.xml
diffstat 2 files changed, 23 insertions(+), 29 deletions(-) [+]
line wrap: on
line diff
--- a/Sbml2CarbonSkeletonNet.xml	Mon Aug 25 16:07:54 2025 +0000
+++ b/Sbml2CarbonSkeletonNet.xml	Fri Nov 21 10:22:17 2025 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="@TOOL_VERSION@">
-  <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forge.inrae.fr/metexplore/gsam)</description>
+  <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description>
   <macros>
     <import>macros.xml</import>
   </macros>
@@ -23,7 +23,7 @@
 ]]></command>
   <inputs>
     <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
-    <param argument="-g" format="tabular" label="input GSAM file" name="inputAAM" optional="false" type="data" value=""/>
+    <param argument="-g" format="gsam" label="input GSAM file" name="inputAAM" optional="false" type="data" value=""/>
     <param argument="-ks" checked="false" falsevalue="" label="keep edges involving single-carbon compounds, such as CO2 (requires formulas in SBML)" name="keepSingleCarbon" truevalue="-ks" type="boolean" value="false"/>
     <param argument="-mc" checked="false" falsevalue="" label="merge compartments (requires unique compound names that are consistent across compartments)" name="mergeComp" truevalue="-mc" type="boolean" value="false"/>
     <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
@@ -41,13 +41,7 @@
     <param argument="-fi" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-fi" type="boolean" value="false"/>
   </inputs>
   <outputs>
-    <data format="txt" name="output">
-      <change_format>
-        <when input="format" value="tab" format="tabular" />
-        <when input="format" value="json" format="json" />
-        <when input="format" value="matrix" format="csv" />
-      </change_format>
-    </data>
+    <data format="txt" name="output"/>
   </outputs>
   <tests>
     <test>
@@ -56,8 +50,8 @@
       <param name="format" value="gml"/>
       <output name="output">
         <assert_contents>
-          <has_text text="node" n="111" delta="5"/>
-          <has_text text="edge" n="202" delta="5"/>
+          <has_text delta="5" n="111" text="node"/>
+          <has_text delta="5" n="202" text="edge"/>
         </assert_contents>
       </output>
     </test>
@@ -68,8 +62,8 @@
       <param name="format" value="gml"/>
       <output name="output">
         <assert_contents>
-          <has_text text="node" n="111" delta="5"/>
-          <has_text text="edge" n="205" delta="5"/>
+          <has_text delta="5" n="111" text="node"/>
+          <has_text delta="5" n="205" text="edge"/>
         </assert_contents>
       </output>
     </test>
@@ -80,8 +74,8 @@
       <param name="format" value="gml"/>
       <output name="output">
         <assert_contents>
-          <has_text text="node" n="83" delta="5"/>
-          <has_text text="edge" n="202" delta="5"/>
+          <has_text delta="5" n="83" text="node"/>
+          <has_text delta="5" n="202" text="edge"/>
         </assert_contents>
       </output>
     </test>
@@ -92,8 +86,8 @@
       <param name="format" value="gml"/>
       <output name="output">
         <assert_contents>
-          <has_text text="node" n="111" delta="5"/>
-          <has_text text="edge" n="143" delta="5"/>
+          <has_text delta="5" n="111" text="node"/>
+          <has_text delta="5" n="143" text="edge"/>
         </assert_contents>
       </output>
     </test>
@@ -104,8 +98,8 @@
       <param name="format" value="gml"/>
       <output name="output">
         <assert_contents>
-          <has_text text="node" n="95" delta="5"/>
-          <has_text text="edge" n="202" delta="5"/>
+          <has_text delta="5" n="95" text="node"/>
+          <has_text delta="5" n="202" text="edge"/>
         </assert_contents>
       </output>
     </test>
@@ -116,8 +110,8 @@
       <param name="format" value="gml"/>
       <output name="output">
         <assert_contents>
-          <has_text text="node" n="111" delta="5"/>
-          <has_text text="edge" n="270" delta="5"/>
+          <has_text delta="5" n="111" text="node"/>
+          <has_text delta="5" n="270" text="edge"/>
         </assert_contents>
       </output>
     </test>
@@ -127,8 +121,8 @@
       <param name="format" value="matrix"/>
       <output name="output">
         <assert_contents>
-          <has_n_lines n="112" delta="5"/>
-          <has_n_columns n="112" delta="5" sep=","/>
+          <has_n_lines delta="5" n="112"/>
+          <has_n_columns delta="5" n="112" sep=","/>
         </assert_contents>
       </output>
     </test>
@@ -139,13 +133,13 @@
       <param name="format" value="gml"/>
       <output name="output">
         <assert_contents>
-          <has_text text="node" n="112" delta="5"/>
-          <has_text text="edge" n="203" delta="5"/>
+          <has_text delta="5" n="112" text="node"/>
+          <has_text delta="5" n="203" text="edge"/>
         </assert_contents>
       </output>
     </test>
   </tests>
-  <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forge.inrae.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.
+  <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.
 @ATTRIBUTION@]]></help>
   <citations/>
 </tool>
--- a/macros.xml	Mon Aug 25 16:07:54 2025 +0000
+++ b/macros.xml	Fri Nov 21 10:22:17 2025 +0000
@@ -3,7 +3,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.1.0">met4j</requirement>
+            <requirement type="package" version="2.2.0">met4j</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -12,10 +12,10 @@
             <xref type="bio.tools">met4j</xref>
         </xrefs>
     </xml>
-    <token name="@TOOL_VERSION@">2.1.0</token>
+    <token name="@TOOL_VERSION@">2.2.0</token>
     <token name="@ATTRIBUTION@"><![CDATA[
 **Attribution**
 
-This Galaxy tool relies on the met4j toolkit which is dedicated to the structural analysis of metabolic networks (https://forge.inrae.fr/metexplore/met4j)
+This Galaxy tool relies on the met4j toolkit which is dedicated to the structural analysis of metabolic networks (https://forgemia.inra.fr/metexplore/met4j)
     ]]></token>
 </macros>
\ No newline at end of file