<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_GetBiggModelProteome" name="GetBiggModelProteome" version="develop">
  <description>Get proteome in fasta format of a model present in the BIGG database</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 bigg.GetBiggModelProteome -m "$modelId"
 -o "$outputFile"
]]></command>
  <inputs>
    <param argument="-m" label="[ex: iMM904] id of the BIGG model" name="modelId" optional="false" type="text" value="iMM904">
      <sanitizer invalid_char="_">
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
  </inputs>
  <outputs>
    <data format="fasta" name="outputFile"/>
  </outputs>
  <tests>
    <test maxseconds="120">
                                    			
      
      
      
      
      
      <param name="modelId" value="e_coli_core"/>
                                    			
      
      
      
      
      
      <output ftype="fasta" name="outputFile">
                                                				
        
        
        
        
        
        <assert_contents>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*name=.*" n="136"/>
                                                            				
        
        
        
        
        
        </assert_contents>
                                                			
      
      
      
      
      
      </output>
                                    		
    
    
    
    
    
    </test>
  </tests>
  <help><![CDATA[Get proteome in fasta format of a model present in the BIGG database]]></help>
  <citations>
    <citation type="doi">10.1093/nar/gkv1049</citation>
  </citations>
</tool>