Mercurial > repos > metexplore > met4j
comparison tools/attributes/SetIds/SetIds.xml @ 9:0976a6257300 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
| author | metexplore |
|---|---|
| date | Fri, 31 Jan 2025 18:28:53 +0000 |
| parents | |
| children | 6a112eaf8f38 |
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| 8:1274e2a62479 | 9:0976a6257300 |
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| 1 <?xml version="1.0" encoding="UTF-8" standalone="no"?> | |
| 2 <tool id="met4j_SetIds" name="SetIds" version="develop"> | |
| 3 <description>Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids</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 attributes.SetIds#if str($colname) != 'nan': | |
| 11 -cnew "$colname" | |
| 12 #end if | |
| 13 #if str($colid): | |
| 14 -ci "$colid" | |
| 15 #end if | |
| 16 $p | |
| 17 $s | |
| 18 #if str($o): | |
| 19 -t "$o" | |
| 20 #end if | |
| 21 #if str($nSkip): | |
| 22 -n "$nSkip" | |
| 23 #end if | |
| 24 -i "$sbml" | |
| 25 #if str($tab) != 'None': | |
| 26 -tab "$tab" | |
| 27 #end if | |
| 28 #if str($c): | |
| 29 -c "$c" | |
| 30 #end if | |
| 31 -o "$out" | |
| 32 ]]></command> | |
| 33 <inputs> | |
| 34 <param argument="-cnew" label="[2] number of the column where are the new ids" name="colname" optional="true" type="integer" value="2"/> | |
| 35 <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1"> | |
| 36 <sanitizer invalid_char="_"> | |
| 37 <valid initial="string.printable"/> | |
| 38 </sanitizer> | |
| 39 </param> | |
| 40 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/> | |
| 41 <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/> | |
| 42 <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION"> | |
| 43 <sanitizer invalid_char="_"> | |
| 44 <valid initial="string.printable"/> | |
| 45 </sanitizer> | |
| 46 </param> | |
| 47 <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0"> | |
| 48 <sanitizer invalid_char="_"> | |
| 49 <valid initial="string.printable"/> | |
| 50 </sanitizer> | |
| 51 </param> | |
| 52 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/> | |
| 53 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/> | |
| 54 <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#"> | |
| 55 <sanitizer invalid_char="_"> | |
| 56 <valid initial="string.printable"/> | |
| 57 </sanitizer> | |
| 58 </param> | |
| 59 </inputs> | |
| 60 <outputs> | |
| 61 <data format="sbml" name="out"/> | |
| 62 </outputs> | |
| 63 <tests> | |
| 64 <test> | |
| 65 | |
| 66 | |
| 67 | |
| 68 | |
| 69 | |
| 70 | |
| 71 <param name="sbml" value="toy_model.xml"/> | |
| 72 | |
| 73 | |
| 74 | |
| 75 | |
| 76 | |
| 77 | |
| 78 <param name="tab" value="idMetabolites.tsv"/> | |
| 79 | |
| 80 | |
| 81 | |
| 82 | |
| 83 | |
| 84 | |
| 85 <param name="o" value="METABOLITE"/> | |
| 86 | |
| 87 | |
| 88 | |
| 89 | |
| 90 | |
| 91 | |
| 92 <output ftype="sbml" name="out"> | |
| 93 | |
| 94 | |
| 95 | |
| 96 | |
| 97 | |
| 98 | |
| 99 <assert_contents> | |
| 100 | |
| 101 | |
| 102 | |
| 103 | |
| 104 | |
| 105 | |
| 106 <is_valid_xml/> | |
| 107 | |
| 108 | |
| 109 | |
| 110 | |
| 111 | |
| 112 | |
| 113 <has_line_matching expression=".*id=.metaboliteA.*" n="1"/> | |
| 114 | |
| 115 | |
| 116 | |
| 117 | |
| 118 | |
| 119 | |
| 120 <has_line_matching expression=".*id=.metaboliteB.*" n="1"/> | |
| 121 | |
| 122 | |
| 123 | |
| 124 | |
| 125 | |
| 126 | |
| 127 </assert_contents> | |
| 128 | |
| 129 | |
| 130 | |
| 131 | |
| 132 | |
| 133 | |
| 134 </output> | |
| 135 | |
| 136 | |
| 137 | |
| 138 | |
| 139 | |
| 140 | |
| 141 </test> | |
| 142 <test> | |
| 143 | |
| 144 | |
| 145 | |
| 146 | |
| 147 | |
| 148 | |
| 149 <param name="sbml" value="toy_model.xml"/> | |
| 150 | |
| 151 | |
| 152 | |
| 153 | |
| 154 | |
| 155 | |
| 156 <param name="tab" value="idReactions.tsv"/> | |
| 157 | |
| 158 | |
| 159 | |
| 160 | |
| 161 | |
| 162 | |
| 163 <output ftype="sbml" name="out"> | |
| 164 | |
| 165 | |
| 166 | |
| 167 | |
| 168 | |
| 169 | |
| 170 <assert_contents> | |
| 171 | |
| 172 | |
| 173 | |
| 174 | |
| 175 | |
| 176 | |
| 177 <is_valid_xml/> | |
| 178 | |
| 179 | |
| 180 | |
| 181 | |
| 182 | |
| 183 | |
| 184 <has_line_matching expression=".*id=.reaction1.*" n="1"/> | |
| 185 | |
| 186 | |
| 187 | |
| 188 | |
| 189 | |
| 190 | |
| 191 <has_line_matching expression=".*id=.reaction2.*" n="1"/> | |
| 192 | |
| 193 | |
| 194 | |
| 195 | |
| 196 | |
| 197 | |
| 198 </assert_contents> | |
| 199 | |
| 200 | |
| 201 | |
| 202 | |
| 203 | |
| 204 | |
| 205 </output> | |
| 206 | |
| 207 | |
| 208 | |
| 209 | |
| 210 | |
| 211 | |
| 212 </test> | |
| 213 <test> | |
| 214 | |
| 215 | |
| 216 | |
| 217 | |
| 218 | |
| 219 | |
| 220 <param name="sbml" value="XF_network.sbml"/> | |
| 221 | |
| 222 | |
| 223 | |
| 224 | |
| 225 | |
| 226 | |
| 227 <param name="tab" value="idPathways.tsv"/> | |
| 228 | |
| 229 | |
| 230 | |
| 231 | |
| 232 | |
| 233 | |
| 234 <param name="o" value="PATHWAY"/> | |
| 235 | |
| 236 | |
| 237 | |
| 238 | |
| 239 | |
| 240 | |
| 241 <output ftype="sbml" name="out"> | |
| 242 | |
| 243 | |
| 244 | |
| 245 | |
| 246 | |
| 247 | |
| 248 <assert_contents> | |
| 249 | |
| 250 | |
| 251 | |
| 252 | |
| 253 | |
| 254 | |
| 255 <is_valid_xml/> | |
| 256 | |
| 257 | |
| 258 | |
| 259 | |
| 260 | |
| 261 | |
| 262 <has_line_matching expression=".*groups:id=.CEB.*" n="1"/> | |
| 263 | |
| 264 | |
| 265 | |
| 266 | |
| 267 | |
| 268 | |
| 269 <has_line_matching expression=".*groups:id=.NSP.*" n="1"/> | |
| 270 | |
| 271 | |
| 272 | |
| 273 | |
| 274 | |
| 275 | |
| 276 </assert_contents> | |
| 277 | |
| 278 | |
| 279 | |
| 280 | |
| 281 | |
| 282 | |
| 283 </output> | |
| 284 | |
| 285 | |
| 286 | |
| 287 | |
| 288 | |
| 289 | |
| 290 </test> | |
| 291 <test> | |
| 292 | |
| 293 | |
| 294 | |
| 295 | |
| 296 | |
| 297 | |
| 298 <param name="sbml" value="XF_network.sbml"/> | |
| 299 | |
| 300 | |
| 301 | |
| 302 | |
| 303 | |
| 304 | |
| 305 <param name="tab" value="idGenes.tsv"/> | |
| 306 | |
| 307 | |
| 308 | |
| 309 | |
| 310 | |
| 311 | |
| 312 <param name="o" value="GENE"/> | |
| 313 | |
| 314 | |
| 315 | |
| 316 | |
| 317 | |
| 318 | |
| 319 <output ftype="sbml" name="out"> | |
| 320 | |
| 321 | |
| 322 | |
| 323 | |
| 324 | |
| 325 | |
| 326 <assert_contents> | |
| 327 | |
| 328 | |
| 329 | |
| 330 | |
| 331 | |
| 332 | |
| 333 <is_valid_xml/> | |
| 334 | |
| 335 | |
| 336 | |
| 337 | |
| 338 | |
| 339 | |
| 340 <has_line_matching expression=".*fbc:id=.G1.*" n="1"/> | |
| 341 | |
| 342 | |
| 343 | |
| 344 | |
| 345 | |
| 346 | |
| 347 <has_line_matching expression=".*fbc:id=.G2.*" n="1"/> | |
| 348 | |
| 349 | |
| 350 | |
| 351 | |
| 352 | |
| 353 | |
| 354 </assert_contents> | |
| 355 | |
| 356 | |
| 357 | |
| 358 | |
| 359 | |
| 360 | |
| 361 </output> | |
| 362 | |
| 363 | |
| 364 | |
| 365 | |
| 366 | |
| 367 | |
| 368 </test> | |
| 369 <test> | |
| 370 | |
| 371 | |
| 372 | |
| 373 | |
| 374 | |
| 375 | |
| 376 <param name="sbml" value="XF_network.sbml"/> | |
| 377 | |
| 378 | |
| 379 | |
| 380 | |
| 381 | |
| 382 | |
| 383 <param name="tab" value="idCompartments.tsv"/> | |
| 384 | |
| 385 | |
| 386 | |
| 387 | |
| 388 | |
| 389 | |
| 390 <param name="o" value="COMPARTMENT"/> | |
| 391 | |
| 392 | |
| 393 | |
| 394 | |
| 395 | |
| 396 | |
| 397 <output ftype="sbml" name="out"> | |
| 398 | |
| 399 | |
| 400 | |
| 401 | |
| 402 | |
| 403 | |
| 404 <assert_contents> | |
| 405 | |
| 406 | |
| 407 | |
| 408 | |
| 409 | |
| 410 | |
| 411 <is_valid_xml/> | |
| 412 | |
| 413 | |
| 414 | |
| 415 | |
| 416 | |
| 417 | |
| 418 <has_line_matching expression=".*id=.cytosol.*" n="1"/> | |
| 419 | |
| 420 | |
| 421 | |
| 422 | |
| 423 | |
| 424 | |
| 425 <has_line_matching expression=".*id=.extra.*" n="1"/> | |
| 426 | |
| 427 | |
| 428 | |
| 429 | |
| 430 | |
| 431 | |
| 432 </assert_contents> | |
| 433 | |
| 434 | |
| 435 | |
| 436 | |
| 437 | |
| 438 | |
| 439 </output> | |
| 440 | |
| 441 | |
| 442 | |
| 443 | |
| 444 | |
| 445 | |
| 446 </test> | |
| 447 </tests> | |
| 448 <help><![CDATA[Set new ids to network objects in a SBML file from a tabulated file containing the old ids and the new ids | |
| 449 The ids must correspond between the tabulated file and the SBML file. | |
| 450 If prefix or suffix is different in the SBML file, use the -p or the -s options. | |
| 451 ]]></help> | |
| 452 <citations/> | |
| 453 </tool> |