Mercurial > repos > metexplore > met4j
diff build/tools/SetCharges/SetCharges.xml @ 10:6a112eaf8f38 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
| author | metexplore |
|---|---|
| date | Mon, 03 Feb 2025 15:59:46 +0000 |
| parents | 0976a6257300 |
| children | 40c15b7467f1 |
line wrap: on
line diff
--- a/build/tools/SetCharges/SetCharges.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/SetCharges/SetCharges.xml Mon Feb 03 15:59:46 2025 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> -<tool id="met4j_SetCharges" name="SetCharges" version="develop"> +<tool id="met4j_SetCharges" name="SetCharges" version="2.0.0"> <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</description> <xrefs> <xref type="bio.tools">met4j</xref> </xrefs> <requirements> - <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container> + <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.SetCharges#if str($colcharge) != 'nan': -cc "$colcharge" @@ -50,387 +50,63 @@ </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> <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="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> <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 metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges