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comparison build/tools/Sbml2CarbonSkeletonNet/Sbml2CarbonSkeletonNet.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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children 6a112eaf8f38
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8:1274e2a62479 9:0976a6257300
1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2 <tool id="met4j_Sbml2CarbonSkeletonNet" name="Sbml2CarbonSkeletonNet" version="develop">
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>
5 <xref type="bio.tools">met4j</xref>
6 </xrefs>
7 <requirements>
8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh convert.Sbml2CarbonSkeletonNet -i "$inputPath"
11 -g "$inputAAM"
12 $keepSingleCarbon
13 $mergeComp
14 $mergeEdges
15 $removeIsolated
16 $undirected
17 $computeWeight
18 #if str($format):
19 -f "$format"
20 #end if
21 $main
22 $fromIndexes
23 -o "$output"
24 ]]></command>
25 <inputs>
26 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
27 <param argument="-g" format="gsam" label="input GSAM file" name="inputAAM" optional="false" type="data" value=""/>
28 <param argument="-ks" checked="false" falsevalue="" label="keep edges involving single-carbon compounds, such as CO2 (requires formulas in SBML)" name="keepSingleCarbon" truevalue="-ks" type="boolean" value="false"/>
29 <param argument="-mc" checked="false" falsevalue="" label="merge compartments (requires unique compound names that are consistent across compartments)" name="mergeComp" truevalue="-mc" type="boolean" value="false"/>
30 <param argument="-me" checked="false" falsevalue="" label="merge parallel edges to produce a simple graph" name="mergeEdges" truevalue="-me" type="boolean" value="false"/>
31 <param argument="-ri" checked="false" falsevalue="" label="remove isolated nodes" name="removeIsolated" truevalue="-ri" type="boolean" value="false"/>
32 <param argument="-un" checked="false" falsevalue="" label="create as undirected" name="undirected" truevalue="-un" type="boolean" value="false"/>
33 <param argument="-tp" checked="false" falsevalue="" label="set transition probability as weight" name="computeWeight" truevalue="-tp" type="boolean" value="false"/>
34 <param argument="-f" label="Format of the exported graphTabulated edge list by default (source id &#9; edge type &#9; target id). Other options include GML, JsonGraph, and tabulated node list (label &#9; node id &#9; node type)." name="format" optional="true" type="select" value="tab">
35 <option value="gml">gml</option>
36 <option selected="true" value="tab">tab</option>
37 <option value="nodeList">nodeList</option>
38 <option value="json">json</option>
39 <option value="matrix">matrix</option>
40 </param>
41 <param argument="-main" checked="false" falsevalue="" label="Compute RPAIRS-like tags and keep only main transitions for each reaction" name="main" truevalue="-main" type="boolean" value="false"/>
42 <param argument="-fi" checked="false" falsevalue="" label="Use GSAM output with carbon indexes" name="fromIndexes" truevalue="-fi" type="boolean" value="false"/>
43 </inputs>
44 <outputs>
45 <data format="txt" name="output"/>
46 </outputs>
47 <tests>
48 <test>
49
50
51
52 <param name="inputPath" value="Human-GEM_pathways.xml"/>
53
54
55
56 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
57
58
59
60 <param name="format" value="gml"/>
61
62
63
64 <output name="output">
65
66
67
68 <assert_contents>
69
70
71
72 <has_n_lines n="2602"/>
73
74
75
76 </assert_contents>
77
78
79
80 </output>
81
82
83
84 </test>
85 <test>
86
87
88
89 <param name="inputPath" value="Human-GEM_pathways.xml"/>
90
91
92
93 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
94
95
96
97 <param name="keepSingleCarbon" value="true"/>
98
99
100
101 <param name="format" value="gml"/>
102
103
104
105 <output name="output">
106
107
108
109 <assert_contents>
110
111
112
113 <has_n_lines n="2629"/>
114
115
116
117 </assert_contents>
118
119
120
121 </output>
122
123
124
125 </test>
126 <test>
127
128
129
130 <param name="inputPath" value="Human-GEM_pathways.xml"/>
131
132
133
134 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
135
136
137
138 <param name="mergeComp" value="true"/>
139
140
141
142 <param name="format" value="gml"/>
143
144
145
146 <output name="output">
147
148
149
150 <assert_contents>
151
152
153
154 <has_n_lines n="2406"/>
155
156
157
158 </assert_contents>
159
160
161
162 </output>
163
164
165
166 </test>
167 <test>
168
169
170
171 <param name="inputPath" value="Human-GEM_pathways.xml"/>
172
173
174
175 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
176
177
178
179 <param name="mergeEdges" value="true"/>
180
181
182
183 <param name="format" value="gml"/>
184
185
186
187 <output name="output">
188
189
190
191 <assert_contents>
192
193
194
195 <has_n_lines n="2071"/>
196
197
198
199 </assert_contents>
200
201
202
203 </output>
204
205
206
207 </test>
208 <test>
209
210
211
212 <param name="inputPath" value="Human-GEM_pathways.xml"/>
213
214
215
216 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
217
218
219
220 <param name="removeIsolated" value="true"/>
221
222
223
224 <param name="format" value="gml"/>
225
226
227
228 <output name="output">
229
230
231
232 <assert_contents>
233
234
235
236 <has_n_lines n="2490"/>
237
238
239
240 </assert_contents>
241
242
243
244 </output>
245
246
247
248 </test>
249 <test>
250
251
252
253 <param name="inputPath" value="Human-GEM_pathways.xml"/>
254
255
256
257 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
258
259
260
261 <param name="undirected" value="true"/>
262
263
264
265 <param name="format" value="gml"/>
266
267
268
269 <output name="output">
270
271
272
273 <assert_contents>
274
275
276
277 <has_n_lines n="3214"/>
278
279
280
281 </assert_contents>
282
283
284
285 </output>
286
287
288
289 </test>
290 <test>
291
292
293
294 <param name="inputPath" value="Human-GEM_pathways.xml"/>
295
296
297
298 <param name="inputAAM" value="Human-GEM_pathways-transitions.tab"/>
299
300
301
302 <param name="format" value="matrix"/>
303
304
305
306 <output name="output">
307
308
309
310 <assert_contents>
311
312
313
314 <has_n_lines n="112"/>
315
316
317
318 </assert_contents>
319
320
321
322 </output>
323
324
325
326 </test>
327 <test>
328
329
330
331 <param name="inputPath" value="Human-GEM_pathways.xml"/>
332
333
334
335 <param name="inputAAM" value="Human-GEM_pathways-transitions2.tab"/>
336
337
338
339 <param name="fromIndexes" value="true"/>
340
341
342
343 <param name="format" value="gml"/>
344
345
346
347 <output name="output">
348
349
350
351 <assert_contents>
352
353
354
355 <has_n_lines n="2611"/>
356
357
358
359 </assert_contents>
360
361
362
363 </output>
364
365
366
367 </test>
368 </tests>
369 <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>
370 <citations/>
371 </tool>