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comparison build/tools/ReactionDistanceMatrix/ReactionDistanceMatrix.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_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="2.0.0"> 2 <tool id="met4j_ReactionDistanceMatrix" name="ReactionDistanceMatrix" version="2.0.1">
3 <description>Create a reaction to reaction distance matrix.</description> 3 <description>Create a reaction to reaction 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.ReactionDistanceMatrix -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.ReactionDistanceMatrix -i "$inputPath"
11 #if str($sideCompoundFile) != 'None': 11 #if str($sideCompoundFile) != 'None':
12 -sc "$sideCompoundFile" 12 -sc "$sideCompoundFile"
13 #end if 13 #end if
36 <outputs> 36 <outputs>
37 <data format="csv" name="outputPath"/> 37 <data format="csv" name="outputPath"/>
38 </outputs> 38 </outputs>
39 <tests> 39 <tests>
40 <test> 40 <test>
41 <param name="inputPath" value="toy_model.xml"/> 41
42 <output ftype="csv" name="outputPath"> 42 <param name="inputPath" value="toy_model.xml"/>
43 <assert_contents> 43
44 <output ftype="csv" name="outputPath">
45
46 <assert_contents>
47
44 <has_n_lines n="8"/> 48 <has_n_lines n="8"/>
49
45 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> 50 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
51
46 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/> 52 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,Infinity,Infinity" n="1"/>
53
47 <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/> 54 <has_line_matching expression="reac2,Infinity,0.0,1.0,1.0,2.0,Infinity,Infinity" n="1"/>
48 </assert_contents> 55
49 </output> 56 </assert_contents>
50 </test> 57
51 <test> 58 </output>
52 <param name="inputPath" value="toy_model.xml"/> 59
53 <param name="undirected" value="true"/> 60 </test>
54 <output ftype="csv" name="outputPath"> 61 <test>
55 <assert_contents> 62
63 <param name="inputPath" value="toy_model.xml"/>
64
65 <param name="undirected" value="true"/>
66
67 <output ftype="csv" name="outputPath">
68
69 <assert_contents>
70
56 <has_n_lines n="8"/> 71 <has_n_lines n="8"/>
72
57 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> 73 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
74
58 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/> 75 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
76
59 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/> 77 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0,4.0,3.0" n="1"/>
60 </assert_contents> 78
61 </output> 79 </assert_contents>
62 </test> 80
63 <test> 81 </output>
64 <param name="inputPath" value="toy_model.xml"/> 82
65 <param name="undirected" value="true"/> 83 </test>
84 <test>
85
86 <param name="inputPath" value="toy_model.xml"/>
87
88 <param name="undirected" value="true"/>
89
66 <param name="sideCompoundFile" value="sides.txt"/> 90 <param name="sideCompoundFile" value="sides.txt"/>
67 <output ftype="csv" name="outputPath"> 91
68 <assert_contents> 92 <output ftype="csv" name="outputPath">
93
94 <assert_contents>
95
69 <has_n_lines n="8"/> 96 <has_n_lines n="8"/>
97
70 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/> 98 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5,reac6,reac7" n="1"/>
99
71 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/> 100 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
101
72 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/> 102 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0,5.0,4.0" n="1"/>
103
73 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/> 104 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0,4.0,3.0" n="1"/>
105
74 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/> 106 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0,3.0,2.0" n="1"/>
75 </assert_contents> 107
76 </output> 108 </assert_contents>
77 </test> 109
78 <test> 110 </output>
79 <param name="inputPath" value="toy_model.xml"/> 111
80 <param name="undirected" value="true"/> 112 </test>
113 <test>
114
115 <param name="inputPath" value="toy_model.xml"/>
116
117 <param name="undirected" value="true"/>
118
81 <param name="rExclude" value="rexclude.txt"/> 119 <param name="rExclude" value="rexclude.txt"/>
82 <output ftype="csv" name="outputPath"> 120
83 <assert_contents> 121 <output ftype="csv" name="outputPath">
122
123 <assert_contents>
124
84 <has_n_lines n="6"/> 125 <has_n_lines n="6"/>
126
85 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> 127 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
128
86 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> 129 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
130
87 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/> 131 <has_line_matching expression="reac2,1.0,0.0,1.0,1.0,2.0" n="1"/>
132
88 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/> 133 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
134
89 <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/> 135 <has_line_matching expression="reac4,2.0,1.0,1.0,0.0,1.0" n="1"/>
136
90 <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/> 137 <has_line_matching expression="reac5,3.0,2.0,2.0,1.0,0.0" n="1"/>
91 </assert_contents> 138
92 </output> 139 </assert_contents>
93 </test> 140
94 <test> 141 </output>
95 <param name="inputPath" value="toy_model.xml"/> 142
96 <param name="undirected" value="true"/> 143 </test>
144 <test>
145
146 <param name="inputPath" value="toy_model.xml"/>
147
148 <param name="undirected" value="true"/>
149
97 <param name="sideCompoundFile" value="sides.txt"/> 150 <param name="sideCompoundFile" value="sides.txt"/>
151
98 <param name="rExclude" value="rexclude.txt"/> 152 <param name="rExclude" value="rexclude.txt"/>
99 <output ftype="csv" name="outputPath"> 153
100 <assert_contents> 154 <output ftype="csv" name="outputPath">
155
156 <assert_contents>
157
101 <has_n_lines n="6"/> 158 <has_n_lines n="6"/>
159
102 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> 160 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
161
103 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> 162 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
163
104 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/> 164 <has_line_matching expression="reac2,1.0,0.0,1.0,2.0,3.0" n="1"/>
165
105 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/> 166 <has_line_matching expression="reac3,1.0,1.0,0.0,1.0,2.0" n="1"/>
167
106 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/> 168 <has_line_matching expression="reac4,2.0,2.0,1.0,0.0,1.0" n="1"/>
169
107 <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/> 170 <has_line_matching expression="reac5,3.0,3.0,2.0,1.0,0.0" n="1"/>
108 </assert_contents> 171
109 </output> 172 </assert_contents>
110 </test> 173
111 <test> 174 </output>
112 <param name="inputPath" value="toy_model.xml"/> 175
176 </test>
177 <test>
178
179 <param name="inputPath" value="toy_model.xml"/>
180
113 <param name="sideCompoundFile" value="sides.txt"/> 181 <param name="sideCompoundFile" value="sides.txt"/>
182
114 <param name="rExclude" value="rexclude.txt"/> 183 <param name="rExclude" value="rexclude.txt"/>
115 <output ftype="csv" name="outputPath"> 184
116 <assert_contents> 185 <output ftype="csv" name="outputPath">
186
187 <assert_contents>
188
117 <has_n_lines n="6"/> 189 <has_n_lines n="6"/>
190
118 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/> 191 <has_line_matching expression="id,reac1,reac2,reac3,reac4,reac5" n="1"/>
192
119 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/> 193 <has_line_matching expression="reac1,0.0,1.0,1.0,2.0,3.0" n="1"/>
194
120 <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/> 195 <has_line_matching expression="reac2,Infinity,0.0,1.0,2.0,3.0" n="1"/>
196
121 <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/> 197 <has_line_matching expression="reac3,Infinity,Infinity,0.0,1.0,2.0" n="1"/>
198
122 <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/> 199 <has_line_matching expression="reac4,Infinity,Infinity,Infinity,0.0,1.0" n="1"/>
200
123 <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/> 201 <has_line_matching expression="reac5,Infinity,Infinity,Infinity,Infinity,0.0" n="1"/>
124 </assert_contents> 202
125 </output> 203 </assert_contents>
204
205 </output>
206
126 </test> 207 </test>
127 </tests> 208 </tests>
128 <help><![CDATA[Create a reaction to reaction distance matrix. 209 <help><![CDATA[Create a reaction to reaction distance matrix.
129 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. 210 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.
130 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. 211 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.