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annotate build/tools/ScopeNetwork/ScopeNetwork.xml @ 6:7a6f2380fc1d draft

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author metexplore
date Wed, 17 May 2023 13:26:37 +0000
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6
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="met4j_ScopeNetwork" name="ScopeNetwork" version="1.3.0">
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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:1.3.0</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 $asTable
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21 -o "$output"
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22 ]]></command>
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23 <inputs>
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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=""/>
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25 <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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26 <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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27 <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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28 <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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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"/>
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30 <param argument="-tab" checked="false" falsevalue="" label="Export in tabulated file instead of .GML" name="asTable" truevalue="-tab" type="boolean" value="false"/>
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31 </inputs>
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32 <outputs>
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33 <data format="gml" name="output"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="sbmlFilePath" value="toy_model.xml"/>
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38 <param name="seedsFilePath" value="seeds.txt"/>
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39 <param name="sideCompoundFile" value="sides.txt"/>
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40 <output ftype="gml" name="output">
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41 <assert_contents>
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42 <has_line_matching expression=".*node.*" n="9"/>
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43 <has_line_matching expression=".*edge.*" n="11"/>
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44 </assert_contents>
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45 </output>
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46 </test>
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47 </tests>
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48 <help><![CDATA[Perform a network expansion from a set of compound seeds to create a scope network
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49 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
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50 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>
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51 <citations/>
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52 </tool>