Mercurial > repos > metexplore > met4j

annotate build/tools/DistanceMatrix/DistanceMatrix.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
parents 1274e2a62479
children 6a112eaf8f38
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="develop">
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3 <description>Create a compound to compound distance matrix.</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:develop</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
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11 #if str($sideCompoundFile) != 'None':
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12 -sc "$sideCompoundFile"
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13 #end if
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14 #if str($seedFile) != 'None':
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15 -s "$seedFile"
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16 #end if
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17 $degree
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18 #if str($weightFile) != 'None':
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19 -w "$weightFile"
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20 #end if
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21 $undirected
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22 -o "$outputPath"
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23 ]]></command>
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24 <inputs>
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25 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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26 <param argument="-sc" format="txt" label="an optional file containing list of side compounds to ignore" name="sideCompoundFile" optional="true" type="data" value=""/>
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27 <param argument="-s" format="txt" label="an optional file containing list of compounds of interest. The returned distance matrix contains only the corresponding rows and columns" name="seedFile" optional="true" type="data" value=""/>
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28 <param argument="-dw" checked="false" falsevalue="" label="penalize traversal of hubs by using degree square weighting (-w must not be set)" name="degree" truevalue="-dw" type="boolean" value="false"/>
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29 <param argument="-w" format="tsv" label="an optional file containing weights for compound pairs" name="weightFile" optional="true" type="data" value=""/>
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30 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
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31 </inputs>
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32 <outputs>
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33 <data format="csv" name="outputPath"/>
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34 </outputs>
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35 <tests>
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36 <test>
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48 <param name="inputPath" value="toy_model.xml"/>
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60 <output ftype="csv" name="outputPath">
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72 <assert_contents>
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84 <has_n_lines n="9"/>
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96 <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/>
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108 <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/>
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119
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120 </assert_contents>
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132 </output>
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144 </test>
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145 <test>
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157 <param name="inputPath" value="toy_model.xml"/>
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169 <param name="sideCompoundFile" value="sides.txt"/>
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181 <param name="degree" value="true"/>
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193 <param name="undirected" value="true"/>
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205 <output ftype="csv" name="outputPath">
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217 <assert_contents>
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229 <has_n_lines n="8"/>
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241 <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/>
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253 <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/>
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265 <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/>
9
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277 <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/>
9
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289 <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/>
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6
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301 </assert_contents>
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6
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313 </output>
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6
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325 </test>
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326 </tests>
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327 <help><![CDATA[Create a compound to compound distance matrix.
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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328 The distance between two compounds is computed as the length of the shortest path connecting the two in the compound graph, where two compounds are linked if they are respectively substrate and product of the same reaction.
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329 An optional edge weighting can be used, turning the distances into the sum of edge weights in the lightest path, rather than the length of the shortest path.The default weighting use target's degree squared. Alternatively, custom weighting can be provided in a file. In that case, edges without weight are ignored during path search.
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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330 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.]]></help>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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331 <citations/>
7a6f2380fc1d planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
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332 </tool>