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comparison unipept.xml @ 7:75b3b3d0adbf draft

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"planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
author galaxyp
date Tue, 06 Apr 2021 16:13:57 +0000
parents 917fd3ebc223
children 7863f1abcdda
comparison
equal deleted inserted replaced
6:9aaa46d45472 7:75b3b3d0adbf
1 <tool id="unipept" name="Unipept" version="4.3.0"> 1 <tool id="unipept" name="Unipept" version="4.5.0">
2 <description>retrieve taxonomy for peptides</description> 2 <description>retrieve taxonomy for peptides</description>
3 <macros> 3 <macros>
4 <xml name="equate_il"> 4 <xml name="equate_il">
5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine"> 5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help> 6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
74 #elif str($peptide_src.fmt) == 'mzid': 74 #elif str($peptide_src.fmt) == 'mzid':
75 --mzid="$peptide_src.input_mzid" 75 --mzid="$peptide_src.input_mzid"
76 #elif str($peptide_src.fmt) == 'pepxml': 76 #elif str($peptide_src.fmt) == 'pepxml':
77 --pepxml="$peptide_src.input_pepxml" 77 --pepxml="$peptide_src.input_pepxml"
78 #end if 78 #end if
79 --peptide_match $peptide_match
80 #if $peptide_match == 'report' and $unmatched_aa != 'default':
81 --unmatched_aa $unmatched_aa
82 #end if
79 #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']: 83 #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
80 --json $output_json 84 --json $output_json
81 #end if 85 #end if
82 #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']: 86 #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
83 --ec_json $output_ec_json 87 --ec_json $output_ec_json
199 </when> 203 </when>
200 <when value="pepxml"> 204 <when value="pepxml">
201 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" /> 205 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
202 </when> 206 </when>
203 </conditional> 207 </conditional>
208 <param name="peptide_match" type="select" label="Match input peptides by">
209 <option value="full">Match to the full input peptide</option>
210 <option value="best" selected="true">Best match to tryptic parts of the input peptide</option>
211 <option value="report">Best match to tryptic parts, add tryptic_match column</option>
212 </param>
213 <param name="unmatched_aa" type="select" label="Show tryptic_match as:">
214 <option value="default">List of matched tryptic parts</option>
215 <option value=".">peptide with unmatched AAs as .</option>
216 <option value="x">peptide with unmatched AAs as x</option>
217 </param>
204 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> 218 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
205 <option value="tsv" selected="true">Tabular with one line per peptide</option> 219 <option value="tsv" selected="true">Tabular with one line per peptide</option>
206 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option> 220 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
207 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option> 221 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
208 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option> 222 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
270 <action name="column_names" type="metadata" default="Unmatched Peptide" /> 284 <action name="column_names" type="metadata" default="Unmatched Peptide" />
271 </actions> 285 </actions>
272 </data> 286 </data>
273 </outputs> 287 </outputs>
274 <tests> 288 <tests>
289 <!-- Test-1 -->
275 <test> 290 <test>
276 <param name="api" value="pept2lca"/> 291 <param name="api" value="pept2lca"/>
277 <param name="fmt" value="tabular"/> 292 <param name="fmt" value="tabular"/>
278 <param name="input_tsv" value="tryptic.tsv"/> 293 <param name="input_tsv" value="tryptic.tsv"/>
279 <param name="column" value="2"/> 294 <param name="column" value="2"/>
289 <assert_contents> 304 <assert_contents>
290 <has_text text="QTAMAV" /> 305 <has_text text="QTAMAV" />
291 </assert_contents> 306 </assert_contents>
292 </output> 307 </output>
293 </test> 308 </test>
309 <!-- Test-2 -->
294 <test> 310 <test>
295 <param name="api" value="pept2lca"/> 311 <param name="api" value="pept2lca"/>
296 <param name="fmt" value="fasta"/> 312 <param name="fmt" value="fasta"/>
297 <param name="input_fasta" value="peptide.fa"/> 313 <param name="input_fasta" value="peptide.fa"/>
298 <param name="equate_il" value="True"/> 314 <param name="equate_il" value="True"/>
299 <param name="extra" value="True"/> 315 <param name="extra" value="True"/>
300 <param name="names" value="True"/> 316 <param name="names" value="True"/>
301 <param name="selected_outputs" value="json,tsv"/> 317 <param name="selected_outputs" value="json,tsv"/>
302 <!--
303 -->
304 <output name="output_json"> 318 <output name="output_json">
305 <assert_contents> 319 <assert_contents>
306 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" /> 320 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
307 </assert_contents> 321 </assert_contents>
308 </output> 322 </output>
311 <has_text text="9606" /> 325 <has_text text="9606" />
312 <has_text text="9596" /> 326 <has_text text="9596" />
313 </assert_contents> 327 </assert_contents>
314 </output> 328 </output>
315 </test> 329 </test>
330 <!-- Test-3 -->
316 <test> 331 <test>
317 <param name="api" value="pept2taxa"/> 332 <param name="api" value="pept2taxa"/>
318 <param name="fmt" value="fasta"/> 333 <param name="fmt" value="fasta"/>
319 <param name="input_fasta" value="peptide.fa"/> 334 <param name="input_fasta" value="peptide.fa"/>
320 <param name="equate_il" value="True"/> 335 <param name="equate_il" value="True"/>
326 <has_text text="sapiens" /> 341 <has_text text="sapiens" />
327 <has_text text="paniscus" /> 342 <has_text text="paniscus" />
328 </assert_contents> 343 </assert_contents>
329 </output> 344 </output>
330 </test> 345 </test>
346 <!-- Test-4 -->
331 <test> 347 <test>
332 <param name="api" value="pept2funct"/> 348 <param name="api" value="pept2funct"/>
333 <param name="fmt" value="tabular"/> 349 <param name="fmt" value="tabular"/>
334 <param name="input_tsv" value="input.tsv"/> 350 <param name="input_tsv" value="input.tsv"/>
335 <param name="column" value="2"/> 351 <param name="column" value="2"/>
339 <output name="output_tsv"> 355 <output name="output_tsv">
340 <assert_contents> 356 <assert_contents>
341 <has_text text="GO:0004802" /> 357 <has_text text="GO:0004802" />
342 <has_text text="2.2.1.1" /> 358 <has_text text="2.2.1.1" />
343 <has_text text="IPR005475" /> 359 <has_text text="IPR005475" />
360 </assert_contents>
361 </output>
362 <output name="output_ec_tsv">
363 <assert_contents>
364 <has_text text="2.2.1.1" />
365 </assert_contents>
366 </output>
367 <output name="output_go_tsv">
368 <assert_contents>
369 <has_text text="GO:0004802" />
370 </assert_contents>
371 </output>
372 <output name="output_ipr_tsv">
373 <assert_contents>
374 <has_text text="IPR005475" />
375 </assert_contents>
376 </output>
377 </test>
378 <!-- Test-5 -->
379 <test>
380 <param name="api" value="pept2funct"/>
381 <param name="fmt" value="tabular"/>
382 <param name="input_tsv" value="input.tsv"/>
383 <param name="column" value="2"/>
384 <param name="extra" value="True"/>
385 <param name="names" value="True"/>
386 <param name="peptide_match" value="full"/>
387 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
388 <output name="output_tsv">
389 <assert_contents>
390 <has_text text="GO:0004802" />
391 <has_text text="2.2.1.1" />
392 <has_text text="IPR005475" />
393 <has_text_matching expression="FAPLLEEYKAEDWVQK\t0" />
394 </assert_contents>
395 </output>
396 <output name="output_ec_tsv">
397 <assert_contents>
398 <has_text text="2.2.1.1" />
399 </assert_contents>
400 </output>
401 <output name="output_go_tsv">
402 <assert_contents>
403 <has_text text="GO:0004802" />
404 </assert_contents>
405 </output>
406 <output name="output_ipr_tsv">
407 <assert_contents>
408 <has_text text="IPR005475" />
409 </assert_contents>
410 </output>
411 </test>
412 <!-- Test-6 -->
413 <test>
414 <param name="api" value="pept2funct"/>
415 <param name="fmt" value="tabular"/>
416 <param name="input_tsv" value="input.tsv"/>
417 <param name="column" value="2"/>
418 <param name="extra" value="True"/>
419 <param name="names" value="True"/>
420 <param name="peptide_match" value="report"/>
421 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
422 <output name="output_tsv">
423 <assert_contents>
424 <has_text text="GO:0004802" />
425 <has_text text="2.2.1.1" />
426 <has_text text="IPR005475" />
427 <has_text_matching expression="FAPLLEEYKAEDWVQK\tAEDWVQK\t1" />
344 </assert_contents> 428 </assert_contents>
345 </output> 429 </output>
346 <output name="output_ec_tsv"> 430 <output name="output_ec_tsv">
347 <assert_contents> 431 <assert_contents>
348 <has_text text="2.2.1.1" /> 432 <has_text text="2.2.1.1" />