comparison build/tools/SetReferences/SetReferences.xml @ 11:40c15b7467f1 draft default tip

planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518

10:6a112eaf8f38

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_SetReferences" name="SetReferences" version="2.0.0">
  <description>Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references</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.SetReferences#if str($colRef) != 'nan':
 -cr "$colRef"
#end if
 -ref "$ref"

  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="refs.tsv"/>
      <param name="ref" value="InChi"/>
      <param name="o" value="METABOLITE"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*C2H6O.*" n="3"/>
          <has_line_matching expression=".*C6H8O6.*" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references
Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry)
The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help>

11:40c15b7467f1

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_SetReferences" name="SetReferences" version="2.0.1">
  <description>Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references</description>
  <xrefs>
    <xref type="bio.tools">met4j</xref>
  </xrefs>
  <requirements>
    <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetReferences#if str($colRef) != 'nan':
 -cr "$colRef"
#end if
 -ref "$ref"

  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
            
      <param name="sbml" value="toy_model.xml"/>
            
      <param name="tab" value="refs.tsv"/>
            
      <param name="ref" value="InChi"/>
            
      <param name="o" value="METABOLITE"/>
            
      <output ftype="sbml" name="out">
                
        <assert_contents>
                    
          <is_valid_xml/>
                    
          <has_line_matching expression=".*C2H6O.*" n="3"/>
                    
          <has_line_matching expression=".*C6H8O6.*" n="1"/>
                  
        </assert_contents>
              
      </output>
          
    </test>
  </tests>
  <help><![CDATA[Add references to network objects in a SBML file from a tabulated file containing the metabolite ids and the references
Reference name given as parameter (-ref) must correspond to an existing id in the registry of identifiers.org (https://registry.identifiers.org/registry)
The corresponding key:value pair will be written as metabolite or reaction MIRIAM annotation (see https://pubmed.ncbi.nlm.nih.gov/16333295/)]]></help>