Mercurial > repos > metexplore > met4j
diff tools/networkAnalysis/ChokePoint/ChokePoint.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
| author | metexplore |
|---|---|
| date | Wed, 17 May 2023 13:26:37 +0000 |
| parents | 35c9abcd8934 |
| children | 1436e9cde9c9 |
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--- a/tools/networkAnalysis/ChokePoint/ChokePoint.xml Thu Jan 12 13:45:13 2023 +0000 +++ b/tools/networkAnalysis/ChokePoint/ChokePoint.xml Wed May 17 13:26:37 2023 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_ChokePoint" name="ChokePoint" version="1.2.1"> +<tool id="met4j_ChokePoint" name="ChokePoint" version="MET4J_VERSION_TEST"> <description>Compute the Choke points of a metabolic network.</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.1</container> + <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:MET4J_VERSION_TEST</container> </requirements> <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ChokePoint -i "$inputPath" #if str($sideCompoundFile) != 'None': @@ -22,28 +22,28 @@ </outputs> <tests> <test> - <param name="inputPath" value="XF_network.sbml"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="202"/> - <has_n_columns n="3"/> - <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="1"/> - <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --> M_ru5p_L_c" n="1"/> - </assert_contents> - </output> - </test> + <param name="inputPath" value="XF_network.sbml"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_lines n="202"/> + <has_n_columns n="3"/> + <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="1"/> + <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --> M_ru5p_L_c" n="1"/> + </assert_contents> + </output> + </test> <test> - <param name="inputPath" value="XF_network.sbml"/> - <param name="sideCompoundFile" value="sides.txt"/> - <output ftype="tsv" name="outputPath"> - <assert_contents> - <has_n_lines n="200"/> - <has_n_columns n="3"/> - <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="0"/> - <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --> M_ru5p_L_c" n="0"/> - </assert_contents> - </output> - </test> + <param name="inputPath" value="XF_network.sbml"/> + <param name="sideCompoundFile" value="sides.txt"/> + <output ftype="tsv" name="outputPath"> + <assert_contents> + <has_n_lines n="200"/> + <has_n_columns n="3"/> + <has_line_matching expression="R_ADEtex.*adenine_transport_via_diffusion__extracellular_to_periplasm_.*M_ade_e <==> M_ade_p" n="1" negate="true"/> + <has_line_matching expression="R_X5PL3E.*R_X5PL3E.*M_xu5p_L_c --> M_ru5p_L_c" n="1" negate="true"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Compute the Choke points of a metabolic network. Load points constitute an indicator of lethality and can help identifying drug target Choke points are reactions that are required to consume or produce one compound. Targeting of choke point can lead to the accumulation or the loss of some metabolites, thus choke points constitute an indicator of lethality and can help identifying drug target