comparison build/tools/Sbml2CompoundGraph/Sbml2CompoundGraph.xml @ 10:6a112eaf8f38 draft

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95

9:0976a6257300

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="develop">
  <description>Advanced creation of a compound graph representation of a SBML file content</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 convert.Sbml2CompoundGraph -i "$inputPath"
#if str($inputSide) != 'None':
 -sc "$inputSide"
#end if

  <outputs>
    <data format="txt" name="output"/>
  </outputs>
  <tests>
    <test>
                        
      
      
      <param name="inputPath" value="XF_network.sbml"/>
                        
      
      
      <param name="inputSide" value="XF_network_C_Side.tab"/>
                        
      
      
      <param name="format" value="gml"/>
                        
      
      
      <output name="output">
                                
        
        
        <assert_contents>
                                        
          
          
          <has_line_matching expression=".*node.*" n="1101"/>
                                        
          
          
          <has_line_matching expression=".*edge.*" n="5581"/>
                                      
        
        
        </assert_contents>
                              
      
      
      </output>
                      
    
    
    </test>
    <test>
                        
      
      
      <param name="inputPath" value="XF_network.sbml"/>
                        
      
      
      <param name="inputSide" value="XF_network_C_Side.tab"/>
                        
      
      
      <param name="undirected" value="true"/>
                        
      
      
      <param name="computeWeight" value="true"/>
                        
      
      
      <param name="removeIsolated" value="true"/>
                        
      
      
      <param name="degree" value="true"/>
                        
      
      
      <param name="mergingStrat" value="by_id"/>
                        
      
      
      <param name="format" value="gml"/>
                        
      
      
      <output name="output">
                                
        
        
        <assert_contents>
                                        
          
          
          <has_line_matching expression=".*node.*" n="793"/>
                                        
          
          
          <has_line_matching expression=".*edge.*" n="9372"/>
                                      
        
        
        </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.
While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations.
In contrary to the Sbml2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help>

10:6a112eaf8f38

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_Sbml2CompoundGraph" name="Sbml2CompoundGraph" version="2.0.0">
  <description>Advanced creation of a compound graph representation of a SBML file content</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 convert.Sbml2CompoundGraph -i "$inputPath"
#if str($inputSide) != 'None':
 -sc "$inputSide"
#end if

  <outputs>
    <data format="txt" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="XF_network.sbml"/>
      <param name="inputSide" value="XF_network_C_Side.tab"/>
      <param name="format" value="gml"/>
      <output name="output">
        <assert_contents>
          <has_line_matching expression=".*node.*" n="1101"/>
          <has_line_matching expression=".*edge.*" n="5581"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="XF_network.sbml"/>
      <param name="inputSide" value="XF_network_C_Side.tab"/>
      <param name="undirected" value="true"/>
      <param name="computeWeight" value="true"/>
      <param name="removeIsolated" value="true"/>
      <param name="degree" value="true"/>
      <param name="mergingStrat" value="by_id"/>
      <param name="format" value="gml"/>
      <output name="output">
        <assert_contents>
          <has_line_matching expression=".*node.*" n="793"/>
          <has_line_matching expression=".*edge.*" n="9372"/>
        </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.
While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations.
In contrary to the Sbml2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree weighting to get relevant structure without structural data.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.]]></help>