Mercurial > repos > metexplore > met4j
comparison tools/convert/SbmlWizard/SbmlWizard.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_SbmlWizard" name="SbmlWizard" version="2.0.0"> | 2 <tool id="met4j_SbmlWizard" name="SbmlWizard" version="2.0.1"> |
| 3 <description>General SBML model processing</description> | 3 <description>General SBML model processing</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.SbmlWizard -i "$inputPath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SbmlWizard -i "$inputPath" |
| 11 #if str($inputSide) != 'None': | 11 #if str($inputSide) != 'None': |
| 12 -rc "$inputSide" | 12 -rc "$inputSide" |
| 13 #end if | 13 #end if |
| 54 <outputs> | 54 <outputs> |
| 55 <data format="sbml" name="outputPath"/> | 55 <data format="sbml" name="outputPath"/> |
| 56 </outputs> | 56 </outputs> |
| 57 <tests> | 57 <tests> |
| 58 <test> | 58 <test> |
| 59 | |
| 59 <param name="inputPath" value="Human-GEM_pathways.xml"/> | 60 <param name="inputPath" value="Human-GEM_pathways.xml"/> |
| 61 | |
| 60 <param name="removeIsolated" value="true"/> | 62 <param name="removeIsolated" value="true"/> |
| 63 | |
| 61 <param name="removeNoFlux" value="true"/> | 64 <param name="removeNoFlux" value="true"/> |
| 65 | |
| 62 <param name="mergingStrat" value="by_id"/> | 66 <param name="mergingStrat" value="by_id"/> |
| 67 | |
| 63 <param name="removeDuplicated" value="true"/> | 68 <param name="removeDuplicated" value="true"/> |
| 69 | |
| 64 <param name="exchangeCompToRemove" value="s"/> | 70 <param name="exchangeCompToRemove" value="s"/> |
| 71 | |
| 65 <output ftype="sbml" name="outputPath"> | 72 <output ftype="sbml" name="outputPath"> |
| 73 | |
| 66 <assert_contents> | 74 <assert_contents> |
| 75 | |
| 67 <has_text text="</sbml>"/> | 76 <has_text text="</sbml>"/> |
| 77 | |
| 68 </assert_contents> | 78 </assert_contents> |
| 79 | |
| 69 </output> | 80 </output> |
| 81 | |
| 70 </test> | 82 </test> |
| 71 <test> | 83 <test> |
| 84 | |
| 72 <param name="inputPath" value="XF_network.sbml"/> | 85 <param name="inputPath" value="XF_network.sbml"/> |
| 86 | |
| 73 <param name="removeIsolated" value="true"/> | 87 <param name="removeIsolated" value="true"/> |
| 88 | |
| 74 <param name="removeNoFlux" value="true"/> | 89 <param name="removeNoFlux" value="true"/> |
| 90 | |
| 75 <param name="removeDuplicated" value="true"/> | 91 <param name="removeDuplicated" value="true"/> |
| 92 | |
| 76 <param name="inputSide" value="XF_network_C_Side.tab"/> | 93 <param name="inputSide" value="XF_network_C_Side.tab"/> |
| 94 | |
| 77 <param name="inputReactions" value="XF_network_R_Seed.tab"/> | 95 <param name="inputReactions" value="XF_network_R_Seed.tab"/> |
| 96 | |
| 78 <output ftype="sbml" name="outputPath"> | 97 <output ftype="sbml" name="outputPath"> |
| 98 | |
| 79 <assert_contents> | 99 <assert_contents> |
| 100 | |
| 80 <has_text text="</sbml>"/> | 101 <has_text text="</sbml>"/> |
| 102 | |
| 81 </assert_contents> | 103 </assert_contents> |
| 104 | |
| 82 </output> | 105 </output> |
| 106 | |
| 83 </test> | 107 </test> |
| 84 </tests> | 108 </tests> |
| 85 <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help> | 109 <help><![CDATA[General SBML model processing including compound removal (such as side compounds or isolated compounds), reaction removal (ex. blocked or exchange reaction), and compartment merging]]></help> |
| 86 <citations/> | 110 <citations/> |
| 87 </tool> | 111 </tool> |