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annotate build/tools/ScopeNetwork/ScopeNetwork.xml @ 10:6a112eaf8f38 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 71071300dd662ad01bd064abcf6866a192eeea95
author metexplore
date Mon, 03 Feb 2025 15:59:46 +0000
parents 0976a6257300
children 40c15b7467f1
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="2.0.0">
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3 <description>Perform a network expansion from a set of compound seeds to create a scope network</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.0</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ScopeNetwork -i "$sbmlFilePath"
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11 -s "$seedsFilePath"
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12 #if str($sideCompoundFile) != 'None':
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13 -sc "$sideCompoundFile"
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14 #end if
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15 $includeSides
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16 #if str($reactionToIgnoreFile) != 'None':
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17 -ir "$reactionToIgnoreFile"
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18 #end if
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19 $trace
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20 #if str($format):
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21 -f "$format"
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22 #end if
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23 -o "$output"
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24 ]]></command>
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25 <inputs>
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26 <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=""/>
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27 <param argument="-s" format="txt" label="input seeds file: tabulated file containing node of interest ids" name="seedsFilePath" optional="false" type="data" value=""/>
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28 <param argument="-sc" format="txt" 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=""/>
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29 <param argument="-ssc" checked="false" falsevalue="" label="show side compounds in output network" name="includeSides" truevalue="-ssc" type="boolean" value="false"/>
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30 <param argument="-ir" format="txt" label="an optional file containing list of reaction to ignore (forbid inclusion in scope" name="reactionToIgnoreFile" optional="true" type="data" value=""/>
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31 <param argument="-t" checked="false" falsevalue="" label="trace inclusion step index for each node in output" name="trace" truevalue="-t" type="boolean" value="false"/>
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32 <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
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33 <option value="gml">gml</option>
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34 <option selected="true" value="tab">tab</option>
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35 <option value="nodeList">nodeList</option>
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36 <option value="json">json</option>
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37 <option value="matrix">matrix</option>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data format="txt" name="output"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="sbmlFilePath" value="toy_model.xml"/>
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46 <param name="seedsFilePath" value="seeds.txt"/>
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47 <param name="sideCompoundFile" value="sides.txt"/>
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48 <param name="format" value="gml"/>
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49 <output ftype="txt" name="output">
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50 <assert_contents>
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51 <has_line_matching expression=".*node.*" n="9"/>
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52 <has_line_matching expression=".*edge.*" n="11"/>
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
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58 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]]></help>
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59 <citations>
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60 <citation type="doi">10.1007/s00239-005-0027-1</citation>
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61 </citations>
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62 </tool>