comparison tools/attributes/SetChemicalFormulas/SetChemicalFormulas.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_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.0">
  <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</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.SetChemicalFormulas#if str($colformula) != 'nan':
 -cf "$colformula"
#end if
#if str($colid) != 'nan':

  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="formula.tsv"/>
      <output ftype="sbml" name="out">
        <assert_contents>
          <is_valid_xml/>
          <has_line_matching expression=".*CH6O6.*" n="2"/>
          <has_line_matching expression=".*CH12O4.*" n="2"/>
        </assert_contents>
      </output>
    </test>
    <test expect_failure="true">
      <param name="sbml" value="toy_model.xml"/>
      <param name="tab" value="formulaBad.tsv"/>
    </test>
  </tests>
  <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas
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.

11:40c15b7467f1

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_SetChemicalFormulas" name="SetChemicalFormulas" version="2.0.1">
  <description>Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas</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.SetChemicalFormulas#if str($colformula) != 'nan':
 -cf "$colformula"
#end if
#if str($colid) != 'nan':

  <outputs>
    <data format="sbml" name="out"/>
  </outputs>
  <tests>
    <test>
            
      <param name="sbml" value="toy_model.xml"/>
            
      <param name="tab" value="formula.tsv"/>
            
      <output ftype="sbml" name="out">
                
        <assert_contents>
                    
          <is_valid_xml/>
                    
          <has_line_matching expression=".*CH6O6.*" n="2"/>
                    
          <has_line_matching expression=".*CH12O4.*" n="2"/>
                  
        </assert_contents>
              
      </output>
          
    </test>
    <test expect_failure="true">
            
      <param name="sbml" value="toy_model.xml"/>
            
      <param name="tab" value="formulaBad.tsv"/>
          
    </test>
  </tests>
  <help><![CDATA[Set Formula to network metabolites from a tabulated file containing the metabolite ids and the formulas
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.