Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/SeedsAndTargets/SeedsAndTargets.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_SeedsAndTargets" name="SeedsAndTargets" version="develop"> | 2 <tool id="met4j_SeedsAndTargets" name="SeedsAndTargets" version="2.0.0"> |
| 3 <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</description> | 3 <description>Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology</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 networkAnalysis.SeedsAndTargets -i "$inputPath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.SeedsAndTargets -i "$inputPath" |
| 11 #if str($inputSide) != 'None': | 11 #if str($inputSide) != 'None': |
| 12 -sc "$inputSide" | 12 -sc "$inputSide" |
| 13 #end if | 13 #end if |
| 42 <outputs> | 42 <outputs> |
| 43 <data format="tsv" name="outputPath"/> | 43 <data format="tsv" name="outputPath"/> |
| 44 </outputs> | 44 </outputs> |
| 45 <tests> | 45 <tests> |
| 46 <test> | 46 <test> |
| 47 | |
| 48 | |
| 49 | |
| 50 | |
| 51 | |
| 52 | |
| 53 | |
| 54 | |
| 55 | |
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| 57 | |
| 58 <param name="inputPath" value="XF_network.sbml"/> | 47 <param name="inputPath" value="XF_network.sbml"/> |
| 59 | |
| 60 | |
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| 70 <param name="source" value="true"/> | 48 <param name="source" value="true"/> |
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| 81 | |
| 82 <output ftype="tsv" name="outputPath"> | 49 <output ftype="tsv" name="outputPath"> |
| 83 | |
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| 93 | |
| 94 <assert_contents> | 50 <assert_contents> |
| 95 | |
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| 105 | |
| 106 <has_n_columns n="1"/> | 51 <has_n_columns n="1"/> |
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| 118 <has_n_lines n="109"/> | 52 <has_n_lines n="109"/> |
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| 129 | |
| 130 <has_line_matching expression="M_\S+_\w" n="109"/> | 53 <has_line_matching expression="M_\S+_\w" n="109"/> |
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| 141 | |
| 142 </assert_contents> | 54 </assert_contents> |
| 143 | |
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| 154 </output> | 55 </output> |
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| 165 | |
| 166 </test> | 56 </test> |
| 167 <test> | 57 <test> |
| 168 | |
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| 178 | |
| 179 <param name="inputPath" value="XF_network.sbml"/> | 58 <param name="inputPath" value="XF_network.sbml"/> |
| 180 | |
| 181 | |
| 182 | |
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| 185 | |
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| 190 | |
| 191 <param name="sink" value="true"/> | 59 <param name="sink" value="true"/> |
| 192 | |
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| 203 <param name="useInternal" value="true"/> | 60 <param name="useInternal" value="true"/> |
| 204 | |
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| 215 <param name="comp" value="e"/> | 61 <param name="comp" value="e"/> |
| 216 | |
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| 227 <output ftype="tsv" name="outputPath"> | 62 <output ftype="tsv" name="outputPath"> |
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| 239 <assert_contents> | 63 <assert_contents> |
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| 251 <has_n_columns n="1"/> | 64 <has_n_columns n="1"/> |
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| 263 <has_n_lines n="5"/> | 65 <has_n_lines n="5"/> |
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| 274 | |
| 275 <has_line_matching expression="^M_\S+_\w" n="5"/> | 66 <has_line_matching expression="^M_\S+_\w" n="5"/> |
| 276 | |
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| 286 | |
| 287 </assert_contents> | 67 </assert_contents> |
| 288 | |
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| 298 | |
| 299 </output> | 68 </output> |
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| 311 </test> | 69 </test> |
| 312 <test> | 70 <test> |
| 313 | |
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| 323 | |
| 324 <param name="inputPath" value="XF_network.sbml"/> | 71 <param name="inputPath" value="XF_network.sbml"/> |
| 325 | |
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| 327 | |
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| 336 <param name="sink" value="true"/> | 72 <param name="sink" value="true"/> |
| 337 | |
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| 347 | |
| 348 <param name="useBorensteinAlg" value="true"/> | 73 <param name="useBorensteinAlg" value="true"/> |
| 349 | |
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| 360 <param name="comp" value="e"/> | 74 <param name="comp" value="e"/> |
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| 372 <output ftype="tsv" name="outputPath"> | 75 <output ftype="tsv" name="outputPath"> |
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| 384 <assert_contents> | 76 <assert_contents> |
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| 396 <has_n_columns n="1"/> | 77 <has_n_columns n="1"/> |
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| 408 <has_n_lines n="26"/> | 78 <has_n_lines n="26"/> |
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| 420 <has_line_matching expression="^M_\S+_\w" n="26"/> | 79 <has_line_matching expression="^M_\S+_\w" n="26"/> |
| 421 | |
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| 432 </assert_contents> | 80 </assert_contents> |
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| 444 </output> | 81 </output> |
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| 455 | |
| 456 </test> | 82 </test> |
| 457 </tests> | 83 </tests> |
| 458 <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology | 84 <help><![CDATA[Identify exogenously acquired compounds, exogenously available producible compounds and/or dead ends metabolites from metabolic network topology |
| 459 Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms. | 85 Metabolic seeds and targets are useful for identifying medium requirements and metabolic capability, and thus enable analysis of metabolic ties within communities of organisms. |
| 460 This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment. | 86 This application can use seed definition and SCC-based detection algorithm by Borenstein et al. or, alternatively, degree-based sink and source detection with compartment adjustment. |