comparison tools/convert/SbmlWizard/SbmlWizard.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_SbmlWizard" name="SbmlWizard" version="develop">
  <description>General SBML model processing</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.SbmlWizard -i "$inputPath"
#if str($inputSide) != 'None':
 -rc "$inputSide"
#end if

  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
                                    			
      
      
      
      
      
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
                                    			
      
      
      
      
      
      <param name="removeIsolated" value="true"/>
                                    			
      
      
      
      
      
      <param name="removeNoFlux" value="true"/>
                                    			
      
      
      
      
      
      <param name="mergingStrat" value="by_id"/>
                                    			
      
      
      
      
      
      <param name="removeDuplicated" value="true"/>
                                    			
      
      
      
      
      
      <param name="exchangeCompToRemove" value="s"/>
                                    			
      
      
      
      
      
      <output ftype="sbml" name="outputPath">
                                                				
        
        
        
        
        
        <assert_contents>
                                                            					
          
          
          
          
          
          <has_text text="&lt;/sbml&gt;"/>
                                                            				
        
        
        
        
        
        </assert_contents>
                                                			
      
      
      
      
      
      </output>
                                    		
    
    
    
    
    
    </test>
    <test>
                                    			
      
      
      
      
      
      <param name="inputPath" value="XF_network.sbml"/>
                                    			
      
      
      
      
      
      <param name="removeIsolated" value="true"/>
                                    			
      
      
      
      
      
      <param name="removeNoFlux" value="true"/>
                                    			
      
      
      
      
      
      <param name="removeDuplicated" value="true"/>
                                    			
      
      
      
      
      
      <param name="inputSide" value="XF_network_C_Side.tab"/>
                                    			
      
      
      
      
      
      <param name="inputReactions" value="XF_network_R_Seed.tab"/>
                                    			
      
      
      
      
      
      <output ftype="sbml" name="outputPath">
                                                				
        
        
        
        
        
        <assert_contents>
                                                            					
          
          
          
          
          
          <has_text text="&lt;/sbml&gt;"/>
                                                            				
        
        
        
        
        
        </assert_contents>
                                                			
      
      
      
      
      
      </output>
                                    		
    
    
    
    
    
    </test>
  </tests>
  <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help>
  <citations/>
</tool>

10:6a112eaf8f38

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.0">
  <description>General SBML model processing</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.SbmlWizard -i "$inputPath"
#if str($inputSide) != 'None':
 -rc "$inputSide"
#end if

  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
      <param name="inputPath" value="Human-GEM_pathways.xml"/>
      <param name="removeIsolated" value="true"/>
      <param name="removeNoFlux" value="true"/>
      <param name="mergingStrat" value="by_id"/>
      <param name="removeDuplicated" value="true"/>
      <param name="exchangeCompToRemove" value="s"/>
      <output ftype="sbml" name="outputPath">
        <assert_contents>
          <has_text text="&lt;/sbml&gt;"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="inputPath" value="XF_network.sbml"/>
      <param name="removeIsolated" value="true"/>
      <param name="removeNoFlux" value="true"/>
      <param name="removeDuplicated" value="true"/>
      <param name="inputSide" value="XF_network_C_Side.tab"/>
      <param name="inputReactions" value="XF_network_R_Seed.tab"/>
      <output ftype="sbml" name="outputPath">
        <assert_contents>
          <has_text text="&lt;/sbml&gt;"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help>
  <citations/>
</tool>