Mercurial > repos > metexplore > met4j

comparison build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml @ 11:40c15b7467f1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
equal deleted inserted replaced
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_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.0"> 2 <tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="2.0.1">
3 <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</description> 3 <description>Create a carbon skeleton graph representation of a SBML file content, using GSAM atom-mapping file (see https://forgemia.inra.fr/metexplore/gsam)</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 convert.Sbml2CarbonSkeletonNet -i "$inputPath" 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CarbonSkeletonNet -i "$inputPath"
11 -g "$inputAAM" 11 -g "$inputAAM"
12 $keepSingleCarbon 12 $keepSingleCarbon
13 $mergeComp 13 $mergeComp
44 <outputs> 44 <outputs>
45 <data format="txt" name="output"/> 45 <data format="txt" name="output"/>
46 </outputs> 46 </outputs>
47 <tests> 47 <tests>
48 <test> 48 <test>
49 <param name="inputPath" value="Human-GEM_pathways.xml"/> 49
50 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 50 <param name="inputPath" value="Human-GEM_pathways.xml"/>
51 <param name="format" value="gml"/> 51
52 <output name="output"> 52 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
53 <assert_contents> 53
54 <param name="format" value="gml"/>
55
56 <output name="output">
57
58 <assert_contents>
59
54 <has_n_lines n="2602"/> 60 <has_n_lines n="2602"/>
55 </assert_contents> 61
56 </output> 62 </assert_contents>
57 </test> 63
58 <test> 64 </output>
59 <param name="inputPath" value="Human-GEM_pathways.xml"/> 65
60 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 66 </test>
67 <test>
68
69 <param name="inputPath" value="Human-GEM_pathways.xml"/>
70
71 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
72
61 <param name="keepSingleCarbon" value="true"/> 73 <param name="keepSingleCarbon" value="true"/>
62 <param name="format" value="gml"/> 74
63 <output name="output"> 75 <param name="format" value="gml"/>
64 <assert_contents> 76
77 <output name="output">
78
79 <assert_contents>
80
65 <has_n_lines n="2629"/> 81 <has_n_lines n="2629"/>
66 </assert_contents> 82
67 </output> 83 </assert_contents>
68 </test> 84
69 <test> 85 </output>
70 <param name="inputPath" value="Human-GEM_pathways.xml"/> 86
71 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 87 </test>
88 <test>
89
90 <param name="inputPath" value="Human-GEM_pathways.xml"/>
91
92 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
93
72 <param name="mergeComp" value="true"/> 94 <param name="mergeComp" value="true"/>
73 <param name="format" value="gml"/> 95
74 <output name="output"> 96 <param name="format" value="gml"/>
75 <assert_contents> 97
98 <output name="output">
99
100 <assert_contents>
101
76 <has_n_lines n="2406"/> 102 <has_n_lines n="2406"/>
77 </assert_contents> 103
78 </output> 104 </assert_contents>
79 </test> 105
80 <test> 106 </output>
81 <param name="inputPath" value="Human-GEM_pathways.xml"/> 107
82 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 108 </test>
109 <test>
110
111 <param name="inputPath" value="Human-GEM_pathways.xml"/>
112
113 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
114
83 <param name="mergeEdges" value="true"/> 115 <param name="mergeEdges" value="true"/>
84 <param name="format" value="gml"/> 116
85 <output name="output"> 117 <param name="format" value="gml"/>
86 <assert_contents> 118
119 <output name="output">
120
121 <assert_contents>
122
87 <has_n_lines n="2071"/> 123 <has_n_lines n="2071"/>
88 </assert_contents> 124
89 </output> 125 </assert_contents>
90 </test> 126
91 <test> 127 </output>
92 <param name="inputPath" value="Human-GEM_pathways.xml"/> 128
93 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 129 </test>
130 <test>
131
132 <param name="inputPath" value="Human-GEM_pathways.xml"/>
133
134 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
135
94 <param name="removeIsolated" value="true"/> 136 <param name="removeIsolated" value="true"/>
95 <param name="format" value="gml"/> 137
96 <output name="output"> 138 <param name="format" value="gml"/>
97 <assert_contents> 139
140 <output name="output">
141
142 <assert_contents>
143
98 <has_n_lines n="2490"/> 144 <has_n_lines n="2490"/>
99 </assert_contents> 145
100 </output> 146 </assert_contents>
101 </test> 147
102 <test> 148 </output>
103 <param name="inputPath" value="Human-GEM_pathways.xml"/> 149
104 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 150 </test>
151 <test>
152
153 <param name="inputPath" value="Human-GEM_pathways.xml"/>
154
155 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
156
105 <param name="undirected" value="true"/> 157 <param name="undirected" value="true"/>
106 <param name="format" value="gml"/> 158
107 <output name="output"> 159 <param name="format" value="gml"/>
108 <assert_contents> 160
161 <output name="output">
162
163 <assert_contents>
164
109 <has_n_lines n="3214"/> 165 <has_n_lines n="3214"/>
110 </assert_contents> 166
111 </output> 167 </assert_contents>
112 </test> 168
113 <test> 169 </output>
114 <param name="inputPath" value="Human-GEM_pathways.xml"/> 170
115 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/> 171 </test>
172 <test>
173
174 <param name="inputPath" value="Human-GEM_pathways.xml"/>
175
176 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
177
116 <param name="format" value="matrix"/> 178 <param name="format" value="matrix"/>
117 <output name="output"> 179
118 <assert_contents> 180 <output name="output">
181
182 <assert_contents>
183
119 <has_n_lines n="112"/> 184 <has_n_lines n="112"/>
120 </assert_contents> 185
121 </output> 186 </assert_contents>
122 </test> 187
123 <test> 188 </output>
124 <param name="inputPath" value="Human-GEM_pathways.xml"/> 189
190 </test>
191 <test>
192
193 <param name="inputPath" value="Human-GEM_pathways.xml"/>
194
125 <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/> 195 <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/>
196
126 <param name="fromIndexes" value="true"/> 197 <param name="fromIndexes" value="true"/>
127 <param name="format" value="gml"/> 198
128 <output name="output"> 199 <param name="format" value="gml"/>
129 <assert_contents> 200
201 <output name="output">
202
203 <assert_contents>
204
130 <has_n_lines n="2611"/> 205 <has_n_lines n="2611"/>
131 </assert_contents> 206
132 </output> 207 </assert_contents>
208
209 </output>
210
133 </test> 211 </test>
134 </tests> 212 </tests>
135 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help> 213 <help><![CDATA[Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes. Focusing on links between compounds that share parts of their carbon skeleton allows to avoid many transitions involving side compounds, and removes entities without defined chemical structure. This app produces a Carbon Skeleton Network relevant for graph-based analysis of metabolism, in GML or matrix format, from a SBML and an GSAM atom mapping file. GSAM (see https://forgemia.inra.fr/metexplore/gsam) performs atom mapping at genome-scale level using the Reaction Decoder Tool (https://github.com/asad/ReactionDecoder) and allows to compute the number of conserved atoms of a given type between reactants.This app also enables Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the Carbon Skeleton Network.]]></help>
136 <citations/> 214 <citations/>
137 </tool> 215 </tool>