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comparison ReactionDistanceMatrix.xml @ 3:392f9fe363e8 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 15:31:23 +0000
parents d05c0c639108
children
comparison
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2:54837bf4d91d 3:392f9fe363e8
33 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/> 33 <param argument="-u" checked="false" falsevalue="" label="Ignore reaction direction" name="undirected" truevalue="-u" type="boolean" value="false"/>
34 </inputs> 34 </inputs>
35 <outputs> 35 <outputs>
36 <data format="csv" name="outputPath"/> 36 <data format="csv" name="outputPath"/>
37 </outputs> 37 </outputs>
38 <tests> 38 <tests/>
39 <test>
40 <param name="inputPath" value="toy_model.xml"/>
41 <output ftype="csv" name="outputPath">
42 <assert_contents>
43 <has_n_lines n="8"/>
44 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
45 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>
46 <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>
47 </assert_contents>
48 </output>
49 </test>
50 <test>
51 <param name="inputPath" value="toy_model.xml"/>
52 <param name="undirected" value="true"/>
53 <output ftype="csv" name="outputPath">
54 <assert_contents>
55 <has_n_lines n="8"/>
56 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
57 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
58 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/>
59 </assert_contents>
60 </output>
61 </test>
62 <test>
63 <param name="inputPath" value="toy_model.xml"/>
64 <param name="undirected" value="true"/>
65 <param name="sideCompoundFile" value="sides.txt"/>
66 <output ftype="csv" name="outputPath">
67 <assert_contents>
68 <has_n_lines n="8"/>
69 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
70 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
71 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
72 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/>
73 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/>
74 </assert_contents>
75 </output>
76 </test>
77 <test>
78 <param name="inputPath" value="toy_model.xml"/>
79 <param name="undirected" value="true"/>
80 <param name="rExclude" value="rexclude.txt"/>
81 <output ftype="csv" name="outputPath">
82 <assert_contents>
83 <has_n_lines n="6"/>
84 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
85 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
86 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/>
87 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
88 <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/>
89 <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/>
90 </assert_contents>
91 </output>
92 </test>
93 <test>
94 <param name="inputPath" value="toy_model.xml"/>
95 <param name="undirected" value="true"/>
96 <param name="sideCompoundFile" value="sides.txt"/>
97 <param name="rExclude" value="rexclude.txt"/>
98 <output ftype="csv" name="outputPath">
99 <assert_contents>
100 <has_n_lines n="6"/>
101 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
102 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
103 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/>
104 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
105 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/>
106 <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/>
107 </assert_contents>
108 </output>
109 </test>
110 <test>
111 <param name="inputPath" value="toy_model.xml"/>
112 <param name="sideCompoundFile" value="sides.txt"/>
113 <param name="rExclude" value="rexclude.txt"/>
114 <output ftype="csv" name="outputPath">
115 <assert_contents>
116 <has_n_lines n="6"/>
117 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
118 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
119 <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>
120 <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>
121 <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>
122 <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>
123 </assert_contents>
124 </output>
125 </test>
126 </tests>
127 <help><![CDATA[Create a reaction to reaction distance matrix. 39 <help><![CDATA[Create a reaction to reaction distance matrix.
128 The distance between two reactions is computed as the length of the shortest path connecting the two in the reaction graph, where two reactions are linked if they produce a metabolite consumed by the other or the other way around. 40 The distance between two reactions is computed as the length of the shortest path connecting the two in the reaction graph, where two reactions are linked if they produce a metabolite consumed by the other or the other way around.
129 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. 41 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.
130 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal. 42 If no edge weighting is set, it is recommended to provide a list of side compounds to ignore during network traversal.
131 @ATTRIBUTION@]]></help> 43 @ATTRIBUTION@]]></help>