annotate tools/convert/FbcToNotes/FbcToNotes.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_FbcToNotes" name="FbcToNotes" version="develop">
  <description>Convert FBC package annotations to sbml html notes</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.FbcToNotes -i "$inputPath"
 -o "$outputPath"
]]></command>
  <inputs>
    <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
  </inputs>
  <outputs>
    <data format="sbml" name="outputPath"/>
  </outputs>
  <tests>
    <test>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <param name="inputPath" value="ECOL.xml"/>
                                                                        
      
      
      
      
      
      
      
      
      
      
      <output ftype="sbml" name="outputPath">
                                                                                                
        
        
        
        
        
        
        
        
        
        
        <assert_contents>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <is_valid_xml/>
                                                                                                                        
          
          
          
          
          
          
          
          
          
          
          <has_line_matching expression=".*GENE_ASSOCIATION: b2312.*" n="1"/>
                                                                                                                      
        
        
        
        
        
        
        
        
        
        
        </assert_contents>
                                                                                              
      
      
      
      
      
      
      
      
      
      
      </output>
                                                                      
    
    
    
    
    
    
    
    
    
    
    </test>
  </tests>
  <help><![CDATA[Convert FBC package annotations to sbml html notes (see https://www.degruyter.com/document/doi/10.1515/jib-2017-0082/html)]]></help>
  <citations>
    <citation type="doi">10.1515/jib-2017-0082</citation>
  </citations>
</tool>