Mercurial > repos > metexplore > met4j
comparison tools/convert/Sbml2Tab/Sbml2Tab.xml @ 11:40c15b7467f1 draft default tip
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
| author | metexplore |
|---|---|
| date | Thu, 13 Feb 2025 15:08:22 +0000 |
| parents | 6a112eaf8f38 |
| children |
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| 10:6a112eaf8f38 | 11:40c15b7467f1 |
|---|---|
| 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> | 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> |
| 2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.0"> | 2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.1"> |
| 3 <description>Create a tabulated file listing reaction attributes from a SBML file</description> | 3 <description>Create a tabulated file listing reaction attributes from a SBML file</description> |
| 4 <xrefs> | 4 <xrefs> |
| 5 <xref type="bio.tools">met4j</xref> | 5 <xref type="bio.tools">met4j</xref> |
| 6 </xrefs> | 6 </xrefs> |
| 7 <requirements> | 7 <requirements> |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</container> |
| 9 </requirements> | 9 </requirements> |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): |
| 11 -irr "$i" | 11 -irr "$i" |
| 12 #end if | 12 #end if |
| 13 #if str($r): | 13 #if str($r): |
| 32 <outputs> | 32 <outputs> |
| 33 <data format="tsv" name="out"/> | 33 <data format="tsv" name="out"/> |
| 34 </outputs> | 34 </outputs> |
| 35 <tests> | 35 <tests> |
| 36 <test> | 36 <test> |
| 37 | |
| 37 <param name="in" value="toy_model.xml"/> | 38 <param name="in" value="toy_model.xml"/> |
| 39 | |
| 38 <output ftype="tsv" name="out"> | 40 <output ftype="tsv" name="out"> |
| 41 | |
| 39 <assert_contents> | 42 <assert_contents> |
| 43 | |
| 40 <has_n_lines n="8"/> | 44 <has_n_lines n="8"/> |
| 45 | |
| 41 <has_n_columns n="9"/> | 46 <has_n_columns n="9"/> |
| 47 | |
| 42 <has_text text="2.0 E[c] --> D[c]"/> | 48 <has_text text="2.0 E[c] --> D[c]"/> |
| 49 | |
| 43 <has_text text="A[c] <==> B[c]"/> | 50 <has_text text="A[c] <==> B[c]"/> |
| 51 | |
| 44 </assert_contents> | 52 </assert_contents> |
| 53 | |
| 45 </output> | 54 </output> |
| 55 | |
| 46 </test> | 56 </test> |
| 47 <test> | 57 <test> |
| 58 | |
| 48 <param name="in" value="toy_model.xml"/> | 59 <param name="in" value="toy_model.xml"/> |
| 60 | |
| 49 <param name="i" value="->"/> | 61 <param name="i" value="->"/> |
| 62 | |
| 50 <param name="r" value="="/> | 63 <param name="r" value="="/> |
| 64 | |
| 51 <output ftype="tsv" name="out"> | 65 <output ftype="tsv" name="out"> |
| 66 | |
| 52 <assert_contents> | 67 <assert_contents> |
| 68 | |
| 53 <has_n_lines n="8"/> | 69 <has_n_lines n="8"/> |
| 70 | |
| 54 <has_n_columns n="9"/> | 71 <has_n_columns n="9"/> |
| 72 | |
| 55 <has_text text="2.0 E[c] -> D[c]"/> | 73 <has_text text="2.0 E[c] -> D[c]"/> |
| 74 | |
| 56 <has_text text="A[c] = B[c]"/> | 75 <has_text text="A[c] = B[c]"/> |
| 76 | |
| 57 </assert_contents> | 77 </assert_contents> |
| 78 | |
| 58 </output> | 79 </output> |
| 80 | |
| 59 </test> | 81 </test> |
| 60 </tests> | 82 </tests> |
| 61 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> | 83 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> |
| 62 <citations/> | 84 <citations/> |
| 63 </tool> | 85 </tool> |