Mercurial > repos > metexplore > met4j
comparison build/tools/Sbml2Tab/Sbml2Tab.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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| 9:0976a6257300 | 10:6a112eaf8f38 |
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| 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="develop"> | 2 <tool id="met4j_Sbml2Tab" name="Sbml2Tab" version="2.0.0"> |
| 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:develop</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</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 | |
| 38 | |
| 39 | |
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| 47 | |
| 48 <param name="in" value="toy_model.xml"/> | 37 <param name="in" value="toy_model.xml"/> |
| 49 | |
| 50 | |
| 51 | |
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| 59 | |
| 60 <output ftype="tsv" name="out"> | 38 <output ftype="tsv" name="out"> |
| 61 | |
| 62 | |
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| 71 | |
| 72 <assert_contents> | 39 <assert_contents> |
| 73 | |
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| 83 | |
| 84 <has_n_lines n="8"/> | 40 <has_n_lines n="8"/> |
| 85 | |
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| 95 | |
| 96 <has_n_columns n="9"/> | 41 <has_n_columns n="9"/> |
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| 107 | |
| 108 <has_text text="2.0 E[c] --> D[c]"/> | 42 <has_text text="2.0 E[c] --> D[c]"/> |
| 109 | |
| 110 | |
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| 119 | |
| 120 <has_text text="A[c] <==> B[c]"/> | 43 <has_text text="A[c] <==> B[c]"/> |
| 121 | |
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| 131 | |
| 132 </assert_contents> | 44 </assert_contents> |
| 133 | |
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| 143 | |
| 144 </output> | 45 </output> |
| 145 | |
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| 155 | |
| 156 </test> | 46 </test> |
| 157 <test> | 47 <test> |
| 158 | |
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| 169 <param name="in" value="toy_model.xml"/> | 48 <param name="in" value="toy_model.xml"/> |
| 170 | |
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| 180 | |
| 181 <param name="i" value="->"/> | 49 <param name="i" value="->"/> |
| 182 | |
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| 188 | |
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| 192 | |
| 193 <param name="r" value="="/> | 50 <param name="r" value="="/> |
| 194 | |
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| 204 | |
| 205 <output ftype="tsv" name="out"> | 51 <output ftype="tsv" name="out"> |
| 206 | |
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| 216 | |
| 217 <assert_contents> | 52 <assert_contents> |
| 218 | |
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| 228 | |
| 229 <has_n_lines n="8"/> | 53 <has_n_lines n="8"/> |
| 230 | |
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| 241 <has_n_columns n="9"/> | 54 <has_n_columns n="9"/> |
| 242 | |
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| 246 | |
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| 248 | |
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| 250 | |
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| 252 | |
| 253 <has_text text="2.0 E[c] -> D[c]"/> | 55 <has_text text="2.0 E[c] -> D[c]"/> |
| 254 | |
| 255 | |
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| 264 | |
| 265 <has_text text="A[c] = B[c]"/> | 56 <has_text text="A[c] = B[c]"/> |
| 266 | |
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| 276 | |
| 277 </assert_contents> | 57 </assert_contents> |
| 278 | |
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| 288 | |
| 289 </output> | 58 </output> |
| 290 | |
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| 299 | |
| 300 | |
| 301 </test> | 59 </test> |
| 302 </tests> | 60 </tests> |
| 303 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> | 61 <help><![CDATA[Create a tabulated file listing reaction attributes from a SBML file]]></help> |
| 304 <citations/> | 62 <citations/> |
| 305 </tool> | 63 </tool> |