Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
| author | metexplore |
|---|---|
| date | Fri, 10 Jun 2022 10:31:34 +0000 |
| parents | |
| children | 9b162ee6ff8e |
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| -1:000000000000 | 0:dcd16521b969 |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="0.11.0"> | |
| 3 <description>Perform a network expansion from a set of compound seeds to create a scope network</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:0.11.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath" | |
| 11 -s "$seedsFilePath" | |
| 12 #if str($sideCompoundFile) != 'None': | |
| 13 -sc "$sideCompoundFile" | |
| 14 #end if | |
| 15 $includeSides | |
| 16 #if str($reactionToIgnoreFile) != 'None': | |
| 17 -ir "$reactionToIgnoreFile" | |
| 18 #end if | |
| 19 $trace | |
| 20 -o "$output" | |
| 21 ]]></command> | |
| 22 <inputs> | |
| 23 <param argument="-i" format="sbml" label="input SBML file: path to network used for computing scope, in sbml format." name="sbmlFilePath" optional="false" type="data" value=""/> | |
| 24 <param argument="-s" format="" label="input seeds file: tabulated file containing node of interest ids" name="seedsFilePath" optional="false" type="data" value=""/> | |
| 25 <param argument="-sc" format="" label="an optional file containing list of ubiquitous side compounds to be considered available by default but ignored during expansion" name="sideCompoundFile" optional="true" type="data" value=""/> | |
| 26 <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/> | |
| 27 <param argument="-ir" format="" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/> | |
| 28 <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format="gml" name="output"/> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name="sbmlFilePath" value="toy_model.xml"/> | |
| 36 <param name="seedsFilePath" value="seeds.txt"/> | |
| 37 <param name="sideCompoundFile" value="sides.txt"/> | |
| 38 <output ftype="gml" name="output"> | |
| 39 <assert_contents> | |
| 40 <has_line_matching expression=".*node.*" n="9"/> | |
| 41 <has_line_matching expression=".*edge.*" n="11"/> | |
| 42 </assert_contents> | |
| 43 </output> | |
| 44 </test> | |
| 45 </tests> | |
| 46 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network | |
| 47 The scope of a set of compounds (seed) refer to the maximal metabolic network that can be extended from them,where the extension process consist of adding a reaction to the network if and only if all of its substrates are either a seed or a product of a previously added reaction | |
| 48 For more information, see Handorf, Ebenhöh and Heinrich (2005). *Expanding metabolic networks: scopes of compounds, robustness, and evolution.* Journal of molecular evolution, 61(4), 498-512. (https://doi.org/10.1007/s00239-005-0027-1)]]></help> | |
| 49 </tool> |