comparison tools/attributes/GetGenesFromReactions/GetGenesFromReactions.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_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.0">
  <description>Get gene lists from a list of reactions and a SBML file.</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.GetGenesFromReactions -i "$sbml"
 -r "$reactionFile"
#if str($sep):
 -sep "$sep"

  <outputs>
    <data format="tsv" name="outputFile"/>
  </outputs>
  <tests>
    <test>
      <param name="sbml" value="XF_network.sbml"/>
      <param name="reactionFile" value="XF_network_R_Seed.tab"/>
      <output ftype="tsv" name="outputFile">
        <assert_contents>
          <has_n_lines n="2"/>
          <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
          <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
  <citations/>
</tool>

11:40c15b7467f1

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<tool id="met4j_GetGenesFromReactions" name="GetGenesFromReactions" version="2.0.1">
  <description>Get gene lists from a list of reactions and a SBML file.</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.GetGenesFromReactions -i "$sbml"
 -r "$reactionFile"
#if str($sep):
 -sep "$sep"

  <outputs>
    <data format="tsv" name="outputFile"/>
  </outputs>
  <tests>
    <test>
            
      <param name="sbml" value="XF_network.sbml"/>
            
      <param name="reactionFile" value="XF_network_R_Seed.tab"/>
            
      <output ftype="tsv" name="outputFile">
                
        <assert_contents>
                    
          <has_n_lines n="2"/>
                    
          <has_line_matching expression="R_GLUN.*XFCFBP8418_026750" n="1"/>
                    
          <has_line_matching expression="R_ACGS.*XFCFBP8418_025260" n="1"/>
                  
        </assert_contents>
              
      </output>
          
    </test>
  </tests>
  <help><![CDATA[Get associated gene list from a list of reactions and a SBML file. Parse SBML GPR annotations and output a tab-separated file with one row per gene, associated reaction identifiers from input file in first column, gene identifiers in second column.]]></help>
  <citations/>
</tool>