comparison tools/networkAnalysis/ReactionDistanceMatrix/ReactionDistanceMatrix.xml @ 9:0976a6257300 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273

8:1274e2a62479

<?xml version="1.0" encoding="UTF-8"?>
<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="MET4J_VERSION_TEST">
  <description>Create a reaction to reaction distance matrix.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath"
#if str($sideCompoundFile) != 'None':
 -sc "$sideCompoundFile"
#end if

  <outputs>
    <data format="csv" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <output ftype="csv" name="outputPath">
        <assert_contents>
          <has_n_lines n="8"/>
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>
          <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="undirected" value="true"/>
      <output ftype="csv" name="outputPath">
        <assert_contents>
          <has_n_lines n="8"/>
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
          <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="undirected" value="true"/>
      <param name="sideCompoundFile" value="sides.txt"/>
      <output ftype="csv" name="outputPath">
        <assert_contents>
          <has_n_lines n="8"/>
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
          <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
          <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/>
          <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="undirected" value="true"/>
      <param name="rExclude" value="rexclude.txt"/>
      <output ftype="csv" name="outputPath">
        <assert_contents>
          <has_n_lines n="6"/>
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
          <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/>
          <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
          <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/>
          <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="undirected" value="true"/>
      <param name="sideCompoundFile" value="sides.txt"/>
      <param name="rExclude" value="rexclude.txt"/>
      <output ftype="csv" name="outputPath">
        <assert_contents>
          <has_n_lines n="6"/>
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
          <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/>
          <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
          <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/>
          <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="toy_model.xml"/>
      <param name="sideCompoundFile" value="sides.txt"/>
      <param name="rExclude" value="rexclude.txt"/>
      <output ftype="csv" name="outputPath">
        <assert_contents>
          <has_n_lines n="6"/>
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
          <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>
          <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>
          <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>
          <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a reaction to reaction distance matrix.
The distance between two reactions is computed as the length of the shortest path connecting the two in the reaction graph, where two reactions are linked if they produce a metabolite consumed by the other or the other way around.
An optional edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.The default weighting use target's degree squared. Alternatively, custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.

9:0976a6257300

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="develop">
  <description>Create a reaction to reaction distance matrix.</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath"
#if str($sideCompoundFile) != 'None':
 -sc "$sideCompoundFile"
#end if

  <outputs>
    <data format="csv" name="outputPath"/>
  </outputs>
  <tests>
    <test>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="inputPath" value="toy_model.xml"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <output ftype="csv" name="outputPath">
                                                                                                
        
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_n_lines n="8"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>
                                                                                                                      
        
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                              
      
      
      
      
      
      
      
      
      
      
      </output>
                                                                      
    
    
    
    
    
    
    
    
    
    
    </test>
    <test>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="inputPath" value="toy_model.xml"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="undirected" value="true"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <output ftype="csv" name="outputPath">
                                                                                                
        
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_n_lines n="8"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/>
                                                                                                                      
        
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                              
      
      
      
      
      
      
      
      
      
      
      </output>
                                                                      
    
    
    
    
    
    
    
    
    
    
    </test>
    <test>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="inputPath" value="toy_model.xml"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="undirected" value="true"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="sideCompoundFile" value="sides.txt"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <output ftype="csv" name="outputPath">
                                                                                                
        
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_n_lines n="8"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/>
                                                                                                                      
        
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                              
      
      
      
      
      
      
      
      
      
      
      </output>
                                                                      
    
    
    
    
    
    
    
    
    
    
    </test>
    <test>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="inputPath" value="toy_model.xml"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="undirected" value="true"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="rExclude" value="rexclude.txt"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <output ftype="csv" name="outputPath">
                                                                                                
        
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_n_lines n="6"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/>
                                                                                                                      
        
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                              
      
      
      
      
      
      
      
      
      
      
      </output>
                                                                      
    
    
    
    
    
    
    
    
    
    
    </test>
    <test>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="inputPath" value="toy_model.xml"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="undirected" value="true"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="sideCompoundFile" value="sides.txt"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="rExclude" value="rexclude.txt"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <output ftype="csv" name="outputPath">
                                                                                                
        
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_n_lines n="6"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/>
                                                                                                                      
        
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                              
      
      
      
      
      
      
      
      
      
      
      </output>
                                                                      
    
    
    
    
    
    
    
    
    
    
    </test>
    <test>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="inputPath" value="toy_model.xml"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="sideCompoundFile" value="sides.txt"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="rExclude" value="rexclude.txt"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <output ftype="csv" name="outputPath">
                                                                                                
        
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_n_lines n="6"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>
                                                                                                                      
        
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                              
      
      
      
      
      
      
      
      
      
      
      </output>
                                                                      
    
    
    
    
    
    
    
    
    
    
    </test>
  </tests>
  <help><![CDATA[Create a reaction to reaction distance matrix.
The distance between two reactions is computed as the length of the shortest path connecting the two in the reaction graph, where two reactions are linked if they produce a metabolite consumed by the other or the other way around.
An optional edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.The default weighting use target's degree squared. Alternatively, custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.