Mercurial > repos > metexplore > met4j
comparison build/tools/SBMLwizard/SBMLwizard.xml @ 7:1436e9cde9c9 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 1d31a48bf8328b7a3ad9910971d24b9f453459c5
| author | metexplore |
|---|---|
| date | Tue, 04 Jul 2023 10:21:26 +0000 |
| parents | |
| children | 1274e2a62479 |
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| 6:7a6f2380fc1d | 7:1436e9cde9c9 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_SBMLwizard" name="SBMLwizard" version="1.4.0"> | |
| 3 <description>General SBML model processing</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:1.4.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.SBMLwizard -s "$inputPath" | |
| 11 #if str($inputSide) != 'None': | |
| 12 -rc "$inputSide" | |
| 13 #end if | |
| 14 $removeIsolated | |
| 15 #if str($inputReactions) != 'None': | |
| 16 -rr "$inputReactions" | |
| 17 #end if | |
| 18 $removeNoFlux | |
| 19 #if str($mergingStrat): | |
| 20 -mc "$mergingStrat" | |
| 21 #end if | |
| 22 $removeDuplicated | |
| 23 #if str($exchangeCompToRemove): | |
| 24 -rEX "$exchangeCompToRemove" | |
| 25 #end if | |
| 26 -o "$outputPath" | |
| 27 ]]></command> | |
| 28 <inputs> | |
| 29 <param argument="-s" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> | |
| 30 <param argument="-rc" format="txt" label="file containing identifiers of compounds to remove from the metabolic network" name="inputSide" optional="true" type="data" value=""/> | |
| 31 <param argument="-ric" checked="false" falsevalue="" label="remove isolated compounds (not involved in any reaction)" name="removeIsolated" truevalue="-ric" type="boolean" value="false"/> | |
| 32 <param argument="-rr" format="txt" label="file containing identifiers of reactions to remove from the metabolic network" name="inputReactions" optional="true" type="data" value=""/> | |
| 33 <param argument="-r0" checked="false" falsevalue="" label="remove reactions with lower and upper flux bounds both set to 0.0" name="removeNoFlux" truevalue="-r0" type="boolean" value="false"/> | |
| 34 <param argument="-mc" label="merge compartments using the provided strategy. No merge by default. "by_name" can be used if names are consistent and unambiguous across compartments, "by_id" can be used if compartment suffix is present in compounds identifiers (id in form "xxx_y" with xxx as base identifier and y as compartment label)." name="mergingStrat" optional="true" type="select" value="no"> | |
| 35 <option selected="true" value="no">no</option> | |
| 36 <option value="by_name">by_name</option> | |
| 37 <option value="by_id">by_id</option> | |
| 38 </param> | |
| 39 <param argument="-rdr" checked="false" falsevalue="" label="remove duplicated reactions (same reactants, same GPR)" name="removeDuplicated" truevalue="-rdr" type="boolean" value="false"/> | |
| 40 <param argument="-rEX" label="remove exchange reactions and species from given exchange compartment identifier" name="exchangeCompToRemove" optional="true" type="text" value=""> | |
| 41 <sanitizer invalid_char="_"> | |
| 42 <valid initial="string.printable"/> | |
| 43 </sanitizer> | |
| 44 </param> | |
| 45 </inputs> | |
| 46 <outputs> | |
| 47 <data format="sbml" name="outputPath"/> | |
| 48 </outputs> | |
| 49 <tests> | |
| 50 <test> | |
| 51 <param name="inputPath" value="Human-GEM_pathways.xml"/> | |
| 52 <param name="removeIsolated" value="true"/> | |
| 53 <param name="removeNoFlux" value="true"/> | |
| 54 <param name="mergingStrat" value="by_id"/> | |
| 55 <param name="removeDuplicated" value="true"/> | |
| 56 <param name="exchangeCompToRemove" value="s"/> | |
| 57 <output ftype="sbml" name="outputPath"> | |
| 58 <assert_contents> | |
| 59 <has_text text="</sbml>"/> | |
| 60 </assert_contents> | |
| 61 </output> | |
| 62 </test> | |
| 63 <test> | |
| 64 <param name="inputPath" value="XF_network.sbml"/> | |
| 65 <param name="removeIsolated" value="true"/> | |
| 66 <param name="removeNoFlux" value="true"/> | |
| 67 <param name="removeDuplicated" value="true"/> | |
| 68 <param name="inputSide" value="XF_network_C_Side.tab"/> | |
| 69 <param name="inputReactions" value="XF_network_R_Seed.tab"/> | |
| 70 <output ftype="sbml" name="outputPath"> | |
| 71 <assert_contents> | |
| 72 <has_text text="</sbml>"/> | |
| 73 </assert_contents> | |
| 74 </output> | |
| 75 </test> | |
| 76 </tests> | |
| 77 <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> | |
| 78 <citations/> | |
| 79 </tool> |