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comparison tools/networkAnalysis/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 7a6f2380fc1d
children 6a112eaf8f38
comparison
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="MET4J_VERSION_TEST"> 2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="develop">
3 <description>Create a compound to compound distance matrix.</description> 3 <description>Create a compound to compound distance matrix.</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:MET4J_VERSION_TEST</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.DistanceMatrix -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -sc "$sideCompoundFile" 12 -sc "$sideCompoundFile"
13 #end if 13 #end if
32 <outputs> 32 <outputs>
33 <data format="csv" name="outputPath"/> 33 <data format="csv" name="outputPath"/>
34 </outputs> 34 </outputs>
35 <tests> 35 <tests>
36 <test> 36 <test>
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37 <param name="inputPath" value="toy_model.xml"/> 48 <param name="inputPath" value="toy_model.xml"/>
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38 <output ftype="csv" name="outputPath"> 60 <output ftype="csv" name="outputPath">
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39 <assert_contents> 72 <assert_contents>
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40 <has_n_lines n="9"/> 84 <has_n_lines n="9"/>
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41 <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/> 96 <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/>
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42 <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/> 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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43 </assert_contents> 120 </assert_contents>
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44 </output> 132 </output>
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45 </test> 144 </test>
46 <test> 145 <test>
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47 <param name="inputPath" value="toy_model.xml"/> 157 <param name="inputPath" value="toy_model.xml"/>
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48 <param name="sideCompoundFile" value="sides.txt"/> 169 <param name="sideCompoundFile" value="sides.txt"/>
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49 <param name="degree" value="true"/> 181 <param name="degree" value="true"/>
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50 <param name="undirected" value="true"/> 193 <param name="undirected" value="true"/>
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51 <output ftype="csv" name="outputPath"> 205 <output ftype="csv" name="outputPath">
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52 <assert_contents> 217 <assert_contents>
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53 <has_n_lines n="8"/> 229 <has_n_lines n="8"/>
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54 <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/> 241 <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/>
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55 <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/> 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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56 <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/> 265 <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/>
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57 <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/> 277 <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/>
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58 <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/> 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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59 </assert_contents> 301 </assert_contents>
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60 </output> 313 </output>
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61 </test> 325 </test>
62 </tests> 326 </tests>
63 <help><![CDATA[Create a compound to compound distance matrix. 327 <help><![CDATA[Create a compound to compound distance matrix.
64 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. 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.
65 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. 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.