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comparison DistanceMatrix.xml @ 3:da1468773764 draft default tip

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planemo upload for repository https://forge.inrae.fr/metexplore/met4j-galaxy commit e757d0398a8407d983f1ef3f900b31cafc26e170
author metexplore
date Wed, 21 Jan 2026 15:28:45 +0000
parents c5d875dc43ae
children
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2:ff6b95bafb38 3:da1468773764
29 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> 29 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
30 </inputs> 30 </inputs>
31 <outputs> 31 <outputs>
32 <data format="csv" name="outputPath"/> 32 <data format="csv" name="outputPath"/>
33 </outputs> 33 </outputs>
34 <tests> 34 <tests/>
35 <test>
36 <param name="inputPath" value="toy_model.xml"/>
37 <output ftype="csv" name="outputPath">
38 <assert_contents>
39 <has_n_lines n="9"/>
40 <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/>
41 <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/>
42 </assert_contents>
43 </output>
44 </test>
45 <test>
46 <param name="inputPath" value="toy_model.xml"/>
47 <param name="sideCompoundFile" value="sides.txt"/>
48 <param name="degree" value="true"/>
49 <param name="undirected" value="true"/>
50 <output ftype="csv" name="outputPath">
51 <assert_contents>
52 <has_n_lines n="8"/>
53 <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/>
54 <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/>
55 <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/>
56 <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/>
57 <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/>
58 </assert_contents>
59 </output>
60 </test>
61 </tests>
62 <help><![CDATA[Create a compound to compound distance matrix. 35 <help><![CDATA[Create a compound to compound distance matrix.
63 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. 36 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.
64 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. 37 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.
65 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal. 38 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.
66 @ATTRIBUTION@]]></help> 39 @ATTRIBUTION@]]></help>