annotate tools/attributes/ExtractPathways/ExtractPathways.xml @ 9:0976a6257300 draft

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

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_ExtractPathways" name="ExtractPathways" version="develop">
  <description>Extract pathway(s) from a SBML file and create a sub-network SBML file</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 attributes.ExtractPathways -i "$inputPath"
 -p "$pathwayId"
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
    <param argument="-p" label="pathway identifiers, separated by &quot;+&quot; sign if more than one" name="pathwayId" optional="false" type="text" value="">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="inputPath" value="XF_network.sbml"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="pathwayId" value="Citric_Acid_Cycle+Folate_Metabolism+toto"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <output ftype="sbml" name="outputPath">
                                                                                              
        
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                                      
          
          
          
          
          
          
          
          
          
          
          <is_valid_xml/>
                                                                                                                      
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression=".*&lt;reaction.*" n="17"/>
                                                                                                                      
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression=".*groups:id=.*" n="2"/>
                                                                                                                    
        
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                            
      
      
      
      
      
      
      
      
      
      
      </output>
                                                                      
    
    
    
    
    
    
    
    
    
    
    </test>
  </tests>
  <help><![CDATA[Extract pathway(s) from a SBML file and create a sub-network SBML file]]></help>
  <citations/>
</tool>