Mercurial > repos > metexplore > met4j
diff tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.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 |
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--- a/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Thu Jan 12 13:45:13 2023 +0000 +++ b/tools/attributes/SbmlSetChargesFromFile/SbmlSetChargesFromFile.xml Wed May 17 13:26:37 2023 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="1.2.1"> +<tool id="met4j_SbmlSetChargesFromFile" name="SbmlSetChargesFromFile" version="MET4J_VERSION_TEST"> <description>Set charge 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: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 attributes.SbmlSetChargesFromFile#if str($colcharge) != 'nan': -cc "$colcharge" @@ -50,64 +50,64 @@ </outputs> <tests> <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="charges.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> + <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> + </assert_contents> + </output> + </test> <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="chargesWithComment.tsv"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="0"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="chargesWithComment.tsv"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> + <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> + </assert_contents> + </output> + </test> <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <param name="nSkip" value="1"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="0"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="charges.tsv"/> + <param name="nSkip" value="1"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/> + <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> + </assert_contents> + </output> + </test> <test> - <param name="sbml" value="toy_model.xml"/> - <param name="tab" value="charges.tsv"/> - <param name="ci" value="2"/> - <param name="cc" value="3"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> - <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> - </assert_contents> - </output> - </test> + <param name="sbml" value="toy_model.xml"/> + <param name="tab" value="charges.tsv"/> + <param name="ci" value="2"/> + <param name="cc" value="3"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.2.*" n="1"/> + <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/> + </assert_contents> + </output> + </test> <test> - <param name="sbml" value="XF_network.sbml"/> - <param name="tab" value="chargesXF.tsv"/> - <param name="p" value="true"/> - <param name="s" value="true"/> - <output ftype="sbml" name="out"> - <assert_contents> - <is_valid_xml/> - <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> - </assert_contents> - </output> - </test> + <param name="sbml" value="XF_network.sbml"/> + <param name="tab" value="chargesXF.tsv"/> + <param name="p" value="true"/> + <param name="s" value="true"/> + <output ftype="sbml" name="out"> + <assert_contents> + <is_valid_xml/> + <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[Set charge to network metabolites from a tabulated file containing the metabolite ids and the formulas The charge must be a number. The ids must correspond between the tabulated file and the SBML file.