comparison tools/networkAnalysis/ExtractSubReactionNetwork/ExtractSubReactionNetwork.xml @ 11:40c15b7467f1 draft default tip

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518

10:6a112eaf8f38

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="2.0.0">
  <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
 -s "$sourcePath"
 $undirected
 -t "$targetPath"

  <outputs>
    <data format="txt" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="sourcePath" value="seeds.txt"/>
      <param name="targetPath" value="targets.txt"/>
      <param name="sideCompoundFile" value="sides.txt"/>
      <param name="format" value="gml"/>
      <output ftype="txt" name="output">
        <assert_contents>
          <has_line_matching expression=".*node.*" n="3"/>
          <has_line_matching expression=".*edge.*" n="2"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
The subnetwork corresponds to the part of the network that connects reactions from the first list to reactions from the second list.
Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.]]></help>

11:40c15b7467f1

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_ExtractSubReactionNetwork" name="ExtractSubReactionNetwork" version="2.0.1">
  <description>Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ExtractSubReactionNetwork -i "$inputPath"
 -s "$sourcePath"
 $undirected
 -t "$targetPath"

  <outputs>
    <data format="txt" name="output"/>
  </outputs>
  <tests>
    <test>
            
      <param name="inputPath" value="toy_model.xml"/>
            
      <param name="sourcePath" value="seeds.txt"/>
            
      <param name="targetPath" value="targets.txt"/>
            
      <param name="sideCompoundFile" value="sides.txt"/>
            
      <param name="format" value="gml"/>
            
      <output ftype="txt" name="output">
                
        <assert_contents>
                    
          <has_line_matching expression=".*node.*" n="3"/>
                    
          <has_line_matching expression=".*edge.*" n="2"/>
                  
        </assert_contents>
              
      </output>
          
    </test>
  </tests>
  <help><![CDATA[Create a subnetwork from a metabolic network in SBML format, and two files containing lists of reactions of interests ids, one per row, plus one file of the same format containing side compounds ids.
The subnetwork corresponds to the part of the network that connects reactions from the first list to reactions from the second list.
Sources and targets list can have elements in common. The connecting part can be defined as the union of shortest or k-shortest paths between sources and targets, or the Steiner tree connecting them. Contrary to compound graph, reaction graph often lacks weighting policy for edge relevance. In order to ensure appropriate network density, a list of side compounds to ignore for linking reactions must be provided. An optional edge weight file, if available, can also be used.]]></help>