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planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
author galaxyp
date Sat, 02 Jul 2022 13:46:02 +0000
parents 1137ffa5e479
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4:1137ffa5e479 5:42bc03ed02f6
1 <tool id="unipept" name="Unipept" version="4.5.0"> 1 <tool id="unipept" name="Unipept" version="4.5.1">
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>
337 <param name="names" value="False"/> 337 <param name="names" value="False"/>
338 <param name="selected_outputs" value="tsv"/> 338 <param name="selected_outputs" value="tsv"/>
339 <output name="output_tsv"> 339 <output name="output_tsv">
340 <assert_contents> 340 <assert_contents>
341 <has_text text="sapiens" /> 341 <has_text text="sapiens" />
342 <has_text text="paniscus" /> 342 <has_text text="troglodytes" />
343 </assert_contents> 343 </assert_contents>
344 </output> 344 </output>
345 </test> 345 </test>
346 <!-- Test-4 --> 346 <!-- Test-4 -->
347 <test> 347 <test>
447 <help><![CDATA[ 447 <help><![CDATA[
448 **Unipept** 448 **Unipept**
449 449
450 Retrieve Uniprot and taxanomic information for trypic peptides. 450 Retrieve Uniprot and taxanomic information for trypic peptides.
451 451
452 Unipept API documentation - http://unipept.ugent.be/apidocs 452 Unipept API documentation - https://unipept.ugent.be/apidocs
453 453
454 **Input** 454 **Input**
455 455
456 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets. 456 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.
457 457
462 The match to the most specific tryptic fragment is reported. 462 The match to the most specific tryptic fragment is reported.
463 463
464 464
465 **Unipept APIs** 465 **Unipept APIs**
466 466
467 **pept2prot** - http://unipept.ugent.be/apidocs/pept2prot 467 **pept2prot** - https://unipept.ugent.be/apidocs/pept2prot
468 468
469 Returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab when performing a search with the Tryptic Peptide Analysis in the web interface. 469 Returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab when performing a search with the Tryptic Peptide Analysis in the web interface.
470 470
471 By default, each object contains the following information fields extracted from the UniProt record:: 471 By default, each object contains the following information fields extracted from the UniProt record::
472 472
526 subspecies_id 526 subspecies_id
527 varietas_id 527 varietas_id
528 forma_id 528 forma_id
529 529
530 530
531 **pept2lca** - http://unipept.ugent.be/apidocs/pept2lca 531 **pept2lca** - https://unipept.ugent.be/apidocs/pept2lca
532 532
533 Returns the taxonomic lowest common ancestor for a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface. 533 Returns the taxonomic lowest common ancestor for a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
534 534
535 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: 535 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
536 536
568 species_id 568 species_id
569 subspecies_id 569 subspecies_id
570 varietas_id 570 varietas_id
571 forma_id 571 forma_id
572 572
573 **pept2ec** - http://unipept.ugent.be/apidocs/pept2ec 573 **pept2ec** - https://unipept.ugent.be/apidocs/pept2ec
574 574
575 Returns the functional EC-numbers 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. 575 Returns the functional EC-numbers 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.
576 576
577 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: 577 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
578 578
581 ec_number: EC-number associated with the current tryptic peptide. 581 ec_number: EC-number associated with the current tryptic peptide.
582 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number. 582 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
583 name: Optional, name of the EC-number. Included when the extra parameter is set to true. 583 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
584 584
585 585
586 **pept2go** - http://unipept.ugent.be/apidocs/pept2go 586 **pept2go** - https://unipept.ugent.be/apidocs/pept2go
587 587
588 Returns the functional 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. 588 Returns the functional 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.
589 589
590 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: 590 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
591 591
594 go_term: The GO-term associated with the current tryptic peptide. 594 go_term: The GO-term associated with the current tryptic peptide.
595 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term. 595 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
596 name: Optional, name of the GO-term. Included when the extra parameter is set to true. 596 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
597 597
598 598
599 **pept2interpro** - http://unipept.ugent.be/apidocs/pept2interpro 599 **pept2interpro** - https://unipept.ugent.be/apidocs/pept2interpro
600 600
601 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. 601 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.
602 602
603 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: 603 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
604 604
607 code: InterPro entry code associated with the current tryptic peptide 607 code: InterPro entry code associated with the current tryptic peptide
608 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code. 608 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
609 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true. 609 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
610 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true. 610 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
611 611
612 **pept2funct** - http://unipept.ugent.be/apidocs/pept2funct 612 **pept2funct** - https://unipept.ugent.be/apidocs/pept2funct
613 613
614 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. 614 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.
615 615
616 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy:: 616 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
617 617
633 633
634 The Unipept metaproteomics analysis pipeline 634 The Unipept metaproteomics analysis pipeline
635 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1 635 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
636 Article first published online: 11 FEB 2015 636 Article first published online: 11 FEB 2015
637 DOI: 10.1002/pmic.201400361 637 DOI: 10.1002/pmic.201400361
638 http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400361/abstract;jsessionid=BFF1994E4C14DA73D7C907EB208AD710.f04t04
639 638
640 ]]></help> 639 ]]></help>
641 <citations> 640 <citations>
642 <citation type="doi">doi:10.1002/pmic.201400361</citation> 641 <citation type="doi">doi:10.1002/pmic.201400361</citation>
643 </citations> 642 </citations>