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comparison unipept.xml @ 5:917fd3ebc223 draft

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"planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
author galaxyp
date Thu, 30 Apr 2020 07:39:28 -0400
parents 4953dcd7dd39
children 75b3b3d0adbf
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4:4953dcd7dd39 5:917fd3ebc223
1 <tool id="unipept" name="Unipept" version="4.0.0"> 1 <tool id="unipept" name="Unipept" version="4.3.0">
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>
38 <option value="unmatched">Unmatched peptides</option> 38 <option value="unmatched">Unmatched peptides</option>
39 </param> 39 </param>
40 </xml> 40 </xml>
41 </macros> 41 </macros>
42 <requirements> 42 <requirements>
43 <requirement type="package" version="2.7">python</requirement> 43 <requirement type="package" version="3">python</requirement>
44 </requirements> 44 </requirements>
45 <stdio> 45 <stdio>
46 <exit_code range="1:" /> 46 <exit_code range="1:" />
47 </stdio> 47 </stdio>
48 <command><![CDATA[ 48 <command><![CDATA[
92 --ec_tsv $output_ec_tsv 92 --ec_tsv $output_ec_tsv
93 #end if 93 #end if
94 #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']: 94 #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
95 --go_tsv $output_go_tsv 95 --go_tsv $output_go_tsv
96 #end if 96 #end if
97 #if 'ipr_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2interpro', 'pept2funct', 'peptinfo']:
98 --ipr_tsv $output_ipr_tsv
99 #end if
97 #if 'unmatched' in str($selected_outputs).split(','): 100 #if 'unmatched' in str($selected_outputs).split(','):
98 --unmatched $output_unmatched 101 --unmatched $output_unmatched
99 #end if 102 #end if
100 ]]></command> 103 ]]></command>
101 <inputs> 104 <inputs>
104 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option> 107 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
105 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option> 108 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
106 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option> 109 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
107 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option> 110 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
108 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option> 111 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
112 <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>
109 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option> 113 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
110 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option> 114 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
111 </param> 115 </param>
112 <when value="pept2lca"> 116 <when value="pept2lca">
113 <expand macro="equate_il" /> 117 <expand macro="equate_il" />
137 <help>Return the name of the EC-number. 141 <help>Return the name of the EC-number.
138 </help> 142 </help>
139 </expand> 143 </expand>
140 </when> 144 </when>
141 <when value="pept2go"> 145 <when value="pept2go">
146 <expand macro="equate_il" />
147 <expand macro="extra_true">
148 <help>Return the name of the GO-term.
149 </help>
150 </expand>
151 <expand macro="domains" />
152 </when>
153 <when value="pept2interpro">
142 <expand macro="equate_il" /> 154 <expand macro="equate_il" />
143 <expand macro="extra_true"> 155 <expand macro="extra_true">
144 <help>Return the name of the GO-term. 156 <help>Return the name of the GO-term.
145 </help> 157 </help>
146 </expand> 158 </expand>
192 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs"> 204 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
193 <option value="tsv" selected="true">Tabular with one line per peptide</option> 205 <option value="tsv" selected="true">Tabular with one line per peptide</option>
194 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option> 206 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
195 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option> 207 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
196 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option> 208 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
209 <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option>
197 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option> 210 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
198 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option> 211 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
199 <option value="unmatched">Unmatched peptides</option> 212 <option value="unmatched">Unmatched peptides</option>
200 </param> 213 </param>
201 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/> 214 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
242 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter> 255 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
243 <actions> 256 <actions>
244 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" /> 257 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
245 </actions> 258 </actions>
246 </data> 259 </data>
260 <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv">
261 <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter>
262 <actions>
263 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name" />
264 </actions>
265 </data>
266
247 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched"> 267 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
248 <filter>'unmatched' in selected_outputs</filter> 268 <filter>'unmatched' in selected_outputs</filter>
249 <actions> 269 <actions>
250 <action name="column_names" type="metadata" default="Unmatched Peptide" /> 270 <action name="column_names" type="metadata" default="Unmatched Peptide" />
251 </actions> 271 </actions>
277 <param name="input_fasta" value="peptide.fa"/> 297 <param name="input_fasta" value="peptide.fa"/>
278 <param name="equate_il" value="True"/> 298 <param name="equate_il" value="True"/>
279 <param name="extra" value="True"/> 299 <param name="extra" value="True"/>
280 <param name="names" value="True"/> 300 <param name="names" value="True"/>
281 <param name="selected_outputs" value="json,tsv"/> 301 <param name="selected_outputs" value="json,tsv"/>
302 <!--
303 -->
282 <output name="output_json"> 304 <output name="output_json">
283 <assert_contents> 305 <assert_contents>
284 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" /> 306 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
285 </assert_contents> 307 </assert_contents>
286 </output> 308 </output>
301 <param name="selected_outputs" value="tsv"/> 323 <param name="selected_outputs" value="tsv"/>
302 <output name="output_tsv"> 324 <output name="output_tsv">
303 <assert_contents> 325 <assert_contents>
304 <has_text text="sapiens" /> 326 <has_text text="sapiens" />
305 <has_text text="paniscus" /> 327 <has_text text="paniscus" />
306 <has_text text="Gorilla" />
307 </assert_contents> 328 </assert_contents>
308 </output> 329 </output>
309 </test> 330 </test>
310 <test> 331 <test>
311 <param name="api" value="pept2funct"/> 332 <param name="api" value="pept2funct"/>
312 <param name="fmt" value="tabular"/> 333 <param name="fmt" value="tabular"/>
313 <param name="input_tsv" value="input.tsv"/> 334 <param name="input_tsv" value="input.tsv"/>
314 <param name="column" value="2"/> 335 <param name="column" value="2"/>
315 <param name="extra" value="True"/> 336 <param name="extra" value="True"/>
316 <param name="names" value="True"/> 337 <param name="names" value="True"/>
317 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,unmatched"/> 338 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
318 <output name="output_tsv"> 339 <output name="output_tsv">
319 <assert_contents> 340 <assert_contents>
320 <has_text text="GO:0004802" /> 341 <has_text text="GO:0004802" />
321 <has_text text="2.2.1.1" /> 342 <has_text text="2.2.1.1" />
343 <has_text text="IPR005475" />
322 </assert_contents> 344 </assert_contents>
323 </output> 345 </output>
324 <output name="output_ec_tsv"> 346 <output name="output_ec_tsv">
325 <assert_contents> 347 <assert_contents>
326 <has_text text="2.2.1.1" /> 348 <has_text text="2.2.1.1" />
327 </assert_contents> 349 </assert_contents>
328 </output> 350 </output>
329 <output name="output_go_tsv"> 351 <output name="output_go_tsv">
330 <assert_contents> 352 <assert_contents>
331 <has_text text="GO:0004802" /> 353 <has_text text="GO:0004802" />
354 </assert_contents>
355 </output>
356 <output name="output_ipr_tsv">
357 <assert_contents>
358 <has_text text="IPR005475" />
332 </assert_contents> 359 </assert_contents>
333 </output> 360 </output>
334 </test> 361 </test>
335 </tests> 362 </tests>
336 <help><![CDATA[ 363 <help><![CDATA[
483 go_term: The GO-term associated with the current tryptic peptide. 510 go_term: The GO-term associated with the current tryptic peptide.
484 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term. 511 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
485 name: Optional, name of the GO-term. Included when the extra parameter is set to true. 512 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
486 513
487 514
515 **pept2interpro** - http://unipept.ugent.be/apidocs/pept2interpro
516
517 Returns the functional InterPro entries associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
518
519 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
520
521 peptide: the peptide that matched this record
522 total_protein_count: Total amount of proteins matched with the given peptide
523 code: InterPro entry code associated with the current tryptic peptide
524 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
525 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
526 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
527
488 **pept2funct** - http://unipept.ugent.be/apidocs/pept2funct 528 **pept2funct** - http://unipept.ugent.be/apidocs/pept2funct
489 529
490 Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface. 530 Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
491 531
492 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: 532 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
497 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number. 537 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
498 name: Optional, name of the EC-number. Included when the extra parameter is set to true. 538 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
499 go_term: The GO-term associated with the current tryptic peptide. 539 go_term: The GO-term associated with the current tryptic peptide.
500 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term. 540 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
501 name: Optional, name of the GO-term. Included when the extra parameter is set to true. 541 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
542 code: InterPro entry code associated with the current tryptic peptide
543 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
544 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
545 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
502 546
503 547
504 **Attributions** 548 **Attributions**
505 549
506 The Unipept metaproteomics analysis pipeline 550 The Unipept metaproteomics analysis pipeline