comparison tools/attributes/SetNames/SetNames.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_SetNames" name="SetNames" version="develop">
  <description>Set names to network objects in a SBML file from a tabulated file containing the object ids and the names</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.SetNames#if str($colname) != 'nan':
 -cname "$colname"
#end if
#if str($colid):

  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
                                    			
      
      
      
      
      
      <param name="sbml" value="toy_model.xml"/>
                                    			
      
      
      
      
      
      <param name="tab" value="namesMetabolites.tsv"/>
                                    			
      
      
      
      
      
      <param name="o" value="METABOLITE"/>
                                    			
      
      
      
      
      
      <output ftype="sbml" name="out">
                                                				
        
        
        
        
        
        <assert_contents>
                                                            					
          
          
          
          
          
          <is_valid_xml/>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*metaboliteA.*" n="1"/>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*metaboliteB.*" n="1"/>
                                                            				
        
        
        
        
        
        </assert_contents>
                                                			
      
      
      
      
      
      </output>
                                    		
    
    
    
    
    
    </test>
    <test>
                                    			
      
      
      
      
      
      <param name="sbml" value="toy_model.xml"/>
                                    			
      
      
      
      
      
      <param name="tab" value="namesReactions.tsv"/>
                                    			
      
      
      
      
      
      <output ftype="sbml" name="out">
                                                				
        
        
        
        
        
        <assert_contents>
                                                            					
          
          
          
          
          
          <is_valid_xml/>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*reaction1.*" n="1"/>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*reaction2.*" n="1"/>
                                                            				
        
        
        
        
        
        </assert_contents>
                                                			
      
      
      
      
      
      </output>
                                    		
    
    
    
    
    
    </test>
    <test>
                                    			
      
      
      
      
      
      <param name="sbml" value="XF_network.sbml"/>
                                    			
      
      
      
      
      
      <param name="tab" value="namesPathways.tsv"/>
                                    			
      
      
      
      
      
      <param name="o" value="PATHWAY"/>
                                    			
      
      
      
      
      
      <output ftype="sbml" name="out">
                                                				
        
        
        
        
        
        <assert_contents>
                                                            					
          
          
          
          
          
          <is_valid_xml/>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*groups:name=.CEB.*" n="1"/>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*groups:name=.NSP.*" n="1"/>
                                                            				
        
        
        
        
        
        </assert_contents>
                                                			
      
      
      
      
      
      </output>
                                    		
    
    
    
    
    
    </test>
    <test>
                                    			
      
      
      
      
      
      <param name="sbml" value="XF_network.sbml"/>
                                    			
      
      
      
      
      
      <param name="tab" value="namesGenes.tsv"/>
                                    			
      
      
      
      
      
      <param name="o" value="GENE"/>
                                    			
      
      
      
      
      
      <output ftype="sbml" name="out">
                                                				
        
        
        
        
        
        <assert_contents>
                                                            					
          
          
          
          
          
          <is_valid_xml/>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*fbc:name=.G1.*" n="1"/>
                                                            					
          
          
          
          
          
          <has_line_matching expression=".*fbc:name=.G2.*" n="1"/>
                                                            				
        
        
        
        
        
        </assert_contents>
                                                			
      
      
      
      
      
      </output>
                                    		
    
    
    
    
    
    </test>
  </tests>
  <help><![CDATA[Set names to network objects in a SBML file from a tabulated file containing the object ids and the names
The ids must correspond between the tabulated file and the SBML file.
If prefix or suffix is different in the SBML file, use the -p or the -s options.

10:6a112eaf8f38

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_SetNames" name="SetNames" version="2.0.0">
  <description>Set names to network objects in a SBML file from a tabulated file containing the object ids and the names</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 attributes.SetNames#if str($colname) != 'nan':
 -cname "$colname"
#end if
#if str($colid):

  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="namesMetabolites.tsv"/>
      <param name="o" value="METABOLITE"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*metaboliteA.*" n="1"/>
          <has_line_matching expression=".*metaboliteB.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="namesReactions.tsv"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*reaction1.*" n="1"/>
          <has_line_matching expression=".*reaction2.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="tab" value="namesPathways.tsv"/>
      <param name="o" value="PATHWAY"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*groups:name=.CEB.*" n="1"/>
          <has_line_matching expression=".*groups:name=.NSP.*" n="1"/>
        </assert_contents>
      </output>
    </test>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="tab" value="namesGenes.tsv"/>
      <param name="o" value="GENE"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*fbc:name=.G1.*" n="1"/>
          <has_line_matching expression=".*fbc:name=.G2.*" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Set names to network objects in a SBML file from a tabulated file containing the object ids and the names
The ids must correspond between the tabulated file and the SBML file.
If prefix or suffix is different in the SBML file, use the -p or the -s options.