Mercurial > repos > metexplore > met4j
comparison tools/networkAnalysis/PrecursorNetwork/PrecursorNetwork.xml @ 1:9b162ee6ff8e draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 12798951d21c3b2b13514b38148b2848cb422c95
| author | metexplore |
|---|---|
| date | Mon, 27 Jun 2022 13:41:08 +0000 |
| parents | dcd16521b969 |
| children | e69a78624877 |
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| 0:dcd16521b969 | 1:9b162ee6ff8e |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | 1 <?xml version="1.0" encoding="UTF-8"?> |
| 2 <tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="0.11.0"> | 2 <tool id="met4j_PrecursorNetwork" name="PrecursorNetwork" version="0.12.0"> |
| 3 <description>Perform a network expansion from a set of compound targets to create a precursor network.</description> | 3 <description>Perform a network expansion from a set of compound targets to create a precursor network.</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:0.11.0</container> | 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:0.12.0</container> |
| 9 </requirements> | 9 </requirements> |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" | 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.PrecursorNetwork -i "$sbmlFilePath" |
| 11 -t "$targetsFilePath" | 11 -t "$targetsFilePath" |
| 12 #if str($sideCompoundFile) != 'None': | 12 #if str($sideCompoundFile) != 'None': |
| 13 -sc "$sideCompoundFile" | 13 -sc "$sideCompoundFile" |
| 14 #end if | 14 #end if |
| 15 #if str($reactionToIgnoreFile) != 'None': | 15 #if str($reactionToIgnoreFile) != 'None': |
| 16 -ir "$reactionToIgnoreFile" | 16 -ir "$reactionToIgnoreFile" |
| 17 #end if | 17 #end if |
| 18 -o "$output" | 18 -o "$output" |
| 19 ]]> </command> | 19 ]]></command> |
| 20 <inputs> | 20 <inputs> |
| 21 <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=""/> | 21 <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=""/> |
| 22 <param argument="-t" format="" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/> | 22 <param argument="-t" format="" label="input target file: tabulated file containing node of interest ids" name="targetsFilePath" optional="false" type="data" value=""/> |
| 23 <param argument="-sc" format="" label="an optional file containing list of ubiquitous compounds to be considered already available" name="sideCompoundFile" optional="true" type="data" value=""/> | 23 <param argument="-sc" format="" label="an optional file containing list of ubiquitous compounds to be considered already available" name="sideCompoundFile" optional="true" type="data" value=""/> |
| 24 <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=""/> | 24 <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=""/> |
| 38 </output> | 38 </output> |
| 39 </test> | 39 </test> |
| 40 </tests> | 40 </tests> |
| 41 <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. | 41 <help><![CDATA[Perform a network expansion from a set of compound targets to create a precursor network. |
| 42 The precursor network of a set of compounds (targets) refer to the sub-part of a metabolic network from which a target can be reachedThe network expansion process consist of adding a reaction to the network if any of its products are either a targets or a substrate of a previously added reaction]]></help> | 42 The precursor network of a set of compounds (targets) refer to the sub-part of a metabolic network from which a target can be reachedThe network expansion process consist of adding a reaction to the network if any of its products are either a targets or a substrate of a previously added reaction]]></help> |
| 43 <citations/> | |
| 43 </tool> | 44 </tool> |