Mercurial > repos > metexplore > met4j
comparison build/tools/Sbml2Tab/Sbml2Tab.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 | |
| children | 1436e9cde9c9 |
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| 5:35c9abcd8934 | 6:7a6f2380fc1d |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="1.3.0"> | |
| 3 <description>Create a tabulated file from a SBML file</description> | |
| 4 <xrefs> | |
| 5 <xref type="bio.tools">met4j</xref> | |
| 6 </xrefs> | |
| 7 <requirements> | |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2Tab#if str($i): | |
| 11 -i "$i" | |
| 12 #end if | |
| 13 #if str($r): | |
| 14 -r "$r" | |
| 15 #end if | |
| 16 -in "$in" | |
| 17 -out "$out" | |
| 18 ]]></command> | |
| 19 <inputs> | |
| 20 <param argument="-i" label="[-->] String for irreversible reaction" name="i" optional="true" type="text" value="-->"> | |
| 21 <sanitizer invalid_char="_"> | |
| 22 <valid initial="string.printable"/> | |
| 23 </sanitizer> | |
| 24 </param> | |
| 25 <param argument="-r" label="[<==>] String for reversible reaction" name="r" optional="true" type="text" value="<==>"> | |
| 26 <sanitizer invalid_char="_"> | |
| 27 <valid initial="string.printable"/> | |
| 28 </sanitizer> | |
| 29 </param> | |
| 30 <param argument="-in" format="sbml" label="Sbml file" name="in" optional="false" type="data" value=""/> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="tsv" name="out"/> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="in" value="toy_model.xml"/> | |
| 38 <output ftype="tsv" name="out"> | |
| 39 <assert_contents> | |
| 40 <has_n_lines n="8"/> | |
| 41 <has_n_columns n="9"/> | |
| 42 <has_text text="2.0 E[c] --> D[c]"/> | |
| 43 <has_text text="A[c] <==> B[c]"/> | |
| 44 </assert_contents> | |
| 45 </output> | |
| 46 </test> | |
| 47 <test> | |
| 48 <param name="in" value="toy_model.xml"/> | |
| 49 <param name="i" value="->"/> | |
| 50 <param name="r" value="="/> | |
| 51 <output ftype="tsv" name="out"> | |
| 52 <assert_contents> | |
| 53 <has_n_lines n="8"/> | |
| 54 <has_n_columns n="9"/> | |
| 55 <has_text text="2.0 E[c] -> D[c]"/> | |
| 56 <has_text text="A[c] = B[c]"/> | |
| 57 </assert_contents> | |
| 58 </output> | |
| 59 </test> | |
| 60 </tests> | |
| 61 <help><![CDATA[Create a tabulated file from a SBML file]]></help> | |
| 62 <citations/> | |
| 63 </tool> |