comparison tools/reconstruction/CreateMetaNetwork/CreateMetaNetwork.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_CreateMetaNetwork" name="CreateMetaNetwork" version="develop">
  <description>Create a Meta-Network from two sub-networks in SBML format.</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 reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath"
 -n2 "$sbml2FilePath"
 -n1ex "$external1"
 -n2ex "$external2"

  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
                                                                
      
      
      
      
      
      
      
      
      
      <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/>
                                                                
      
      
      
      
      
      
      
      
      
      <param name="sbml2FilePath" value="ECOL.xml"/>
                                                                
      
      
      
      
      
      
      
      
      
      <param name="external1" value="s"/>
                                                                
      
      
      
      
      
      
      
      
      
      <param name="external2" value="e"/>
                                                                
      
      
      
      
      
      
      
      
      
      <param name="n1prefix" value="hsa"/>
                                                                
      
      
      
      
      
      
      
      
      
      <param name="n2prefix" value="eco"/>
                                                                
      
      
      
      
      
      
      
      
      
      <param name="mergingCriterion" value="by_metanetx"/>
                                                                
      
      
      
      
      
      
      
      
      
      <output ftype="sbml" name="outputPath">
                                                                                      
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                            
          
          
          
          
          
          
          
          
          
          <has_text text="&lt;/sbml&gt;"/>
                                                                                                          
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                    
      
      
      
      
      
      
      
      
      
      </output>
                                                              
    
    
    
    
    
    
    
    
    
    </test>
  </tests>
  <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format.
A meta-network is a single model which contains several sub-networks that remains individualized within the meta-network (as opposed to model fusion), but which can share some of their components with other sub-networks through a shared "medium" compartment.]]></help>
  <citations/>

10:6a112eaf8f38

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_CreateMetaNetwork" name="CreateMetaNetwork" version="2.0.0">
  <description>Create a Meta-Network from two sub-networks in SBML format.</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 reconstruction.CreateMetaNetwork -n1 "$sbml1FilePath"
 -n2 "$sbml2FilePath"
 -n1ex "$external1"
 -n2ex "$external2"

  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml1FilePath" value="Human-GEM_pathways.xml"/>
      <param name="sbml2FilePath" value="ECOL.xml"/>
      <param name="external1" value="s"/>
      <param name="external2" value="e"/>
      <param name="n1prefix" value="hsa"/>
      <param name="n2prefix" value="eco"/>
      <param name="mergingCriterion" value="by_metanetx"/>
      <output ftype="sbml" name="outputPath">
        <assert_contents>
          <has_text text="&lt;/sbml&gt;"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Create a Meta-Network from two sub-networks in SBML format.
A meta-network is a single model which contains several sub-networks that remains individualized within the meta-network (as opposed to model fusion), but which can share some of their components with other sub-networks through a shared "medium" compartment.]]></help>
  <citations/>