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comparison tools/networkAnalysis/DistanceMatrix/DistanceMatrix.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
comparison
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10:6a112eaf8f38 11:40c15b7467f1
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="2.0.0"> 2 <tool id="met4j_DistanceMatrix" name="DistanceMatrix" version="2.0.1">
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:2.0.0</container> 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:2.0.1</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>
37
37 <param name="inputPath" value="toy_model.xml"/> 38 <param name="inputPath" value="toy_model.xml"/>
39
38 <output ftype="csv" name="outputPath"> 40 <output ftype="csv" name="outputPath">
41
39 <assert_contents> 42 <assert_contents>
43
40 <has_n_lines n="9"/> 44 <has_n_lines n="9"/>
45
41 <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/> 46 <has_line_matching expression="id,A,A_ext,B,C,D,D_ext,E,E_ext" n="1"/>
47
42 <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/> 48 <has_line_matching expression="B,1.0,Infinity,0.0,2.0,1.0,2.0,Infinity,Infinity" n="1"/>
49
43 </assert_contents> 50 </assert_contents>
51
44 </output> 52 </output>
53
45 </test> 54 </test>
46 <test> 55 <test>
56
47 <param name="inputPath" value="toy_model.xml"/> 57 <param name="inputPath" value="toy_model.xml"/>
58
48 <param name="sideCompoundFile" value="sides.txt"/> 59 <param name="sideCompoundFile" value="sides.txt"/>
60
49 <param name="degree" value="true"/> 61 <param name="degree" value="true"/>
62
50 <param name="undirected" value="true"/> 63 <param name="undirected" value="true"/>
64
51 <output ftype="csv" name="outputPath"> 65 <output ftype="csv" name="outputPath">
66
52 <assert_contents> 67 <assert_contents>
68
53 <has_n_lines n="8"/> 69 <has_n_lines n="8"/>
70
54 <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/> 71 <has_line_matching expression="id,A,B,C,D,D_ext,E,E_ext" n="1"/>
72
55 <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/> 73 <has_line_matching expression="A,0.0,4.0,4.0,20.0,21.0,24.0,25.0" n="1"/>
74
56 <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/> 75 <has_line_matching expression="B,4.0,0.0,8.0,16.0,17.0,20.0,21.0" n="1"/>
76
57 <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/> 77 <has_line_matching expression="C,4.0,8.0,0.0,16.0,17.0,20.0,21.0" n="1"/>
78
58 <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/> 79 <has_line_matching expression="D,8.0,4.0,4.0,0.0,1.0,4.0,5.0" n="1"/>
80
59 </assert_contents> 81 </assert_contents>
82
60 </output> 83 </output>
84
61 </test> 85 </test>
62 </tests> 86 </tests>
63 <help><![CDATA[Create a compound to compound distance matrix. 87 <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. 88 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. 89 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.