Mercurial > repos > metexplore > met4j
diff build/tools/Tab2Sbml/Tab2Sbml.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 |
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--- a/build/tools/Tab2Sbml/Tab2Sbml.xml Fri Jan 31 18:28:53 2025 +0000 +++ b/build/tools/Tab2Sbml/Tab2Sbml.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_Tab2Sbml" name="Tab2Sbml" version="develop"> +<tool id="met4j_Tab2Sbml" name="Tab2Sbml" version="2.0.0"> <description>Create a Sbml File from a tabulated file that contains the reaction 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: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 convert.Tab2Sbml#if str($colid) != 'nan': -ci "$colid" @@ -76,657 +76,63 @@ </outputs> <tests> <test> - - - - - - - - - - - <param name="in" value="toy_model.tsv"/> - - - - - - - - - - - <output ftype="sbml" name="sbml"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <is_valid_xml/> - - - - - - - - - - - <has_line_matching expression=".*reaction .*" n="7"/> - - - - - - - - - - - <has_line_matching expression=".*species .*" n="8"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="in" value="toy_model_otherColumns.tsv"/> - - - - - - - - - - - <param name="colid" value="2"/> - - - - - - - - - - - <param name="colformula" value="3"/> - - - - - - - - - - - <output ftype="sbml" name="sbml"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <is_valid_xml/> - - - - - - - - - - - <has_line_matching expression=".*reaction .*" n="7"/> - - - - - - - - - - - <has_line_matching expression=".*species .*" n="8"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="in" value="toy_model_otherSigns.tsv"/> - - - - - - - - - - - <param name="i" value="->"/> - - - - - - - - - - - <param name="r" value="="/> - - - - - - - - - - - <output ftype="sbml" name="sbml"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <is_valid_xml/> - - - - - - - - - - - <has_line_matching expression=".*reaction .*" n="7"/> - - - - - - - - - - - <has_line_matching expression=".*species .*" n="8"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="in" value="toy_model.tsv"/> - - - - - - - - - - - <param name="rp" value="true"/> - - - - - - - - - - - <param name="mp" value="true"/> - - - - - - - - - - - <param name="e" value="_e"/> - - - - - - - - - - - <param name="createCompartment" value="true"/> - - - - - - - - - - - <output ftype="sbml" name="sbml"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <is_valid_xml/> - - - - - - - - - - - <has_line_matching expression=".*boundaryCondition=.true.*" n="3"/> - - - - - - - - - - - <has_line_matching expression=".*id=.M_A_ext_e.*" n="1"/> - - - - - - - - - - - <has_line_matching expression=".*id=.R_reac2.*" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> <test> - - - - - - - - - - - <param name="in" value="toy_model.tsv"/> - - - - - - - - - - - <param name="id" value="myModel"/> - - - - - - - - - - - <output ftype="sbml" name="sbml"> - - - - - - - - - - - <assert_contents> - - - - - - - - - - - <is_valid_xml/> - - - - - - - - - - - <has_line_matching expression=".*myModel.*" n="1"/> - - - - - - - - - - - </assert_contents> - - - - - - - - - - - </output> - - - - - - - - - - - </test> </tests> <help><![CDATA[Create a Sbml File from a tabulated file that contains the reaction ids and the formulas]]></help>