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comparison tools/networkAnalysis/ScopeNetwork/ScopeNetwork.xml @ 4:ae4c301919c4 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 2af2c8a0ca9665e1117bb7810bffc105ed39c4f5
author metexplore
date Thu, 17 Nov 2022 07:57:52 +0000
parents 6bd9aad9626d
children 35c9abcd8934
comparison
equal deleted inserted replaced
3:6bd9aad9626d 4:ae4c301919c4
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.1.0"> 2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.2.0">
3 <description>Perform a network expansion from a set of compound seeds to create a scope network</description> 3 <description>Perform a network expansion from a set of compound seeds to create a scope 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:1.1.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.2.0</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
11 -s "$seedsFilePath" 11 -s "$seedsFilePath"
12 #if str($sideCompoundFile) != 'None': 12 #if str($sideCompoundFile) != 'None':
13 -sc "$sideCompoundFile" 13 -sc "$sideCompoundFile"
15 $includeSides 15 $includeSides
16 #if str($reactionToIgnoreFile) != 'None': 16 #if str($reactionToIgnoreFile) != 'None':
17 -ir "$reactionToIgnoreFile" 17 -ir "$reactionToIgnoreFile"
18 #end if 18 #end if
19 $trace 19 $trace
20 $asTable
20 -o "$output" 21 -o "$output"
21 ]]></command> 22 ]]></command>
22 <inputs> 23 <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="-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="-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="-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="-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="-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 <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/>
30 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
29 </inputs> 31 </inputs>
30 <outputs> 32 <outputs>
31 <data format="gml" name="output"/> 33 <data format="gml" name="output"/>
32 </outputs> 34 </outputs>
33 <tests> 35 <tests>