| Previous changeset 7:75b3b3d0adbf (2021-04-06) Next changeset 9:21a560af5913 (2024-03-12) |
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Commit message:
planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5 |
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modified:
unipept.py unipept.xml |
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| diff -r 75b3b3d0adbf -r 7863f1abcdda unipept.py --- a/unipept.py Tue Apr 06 16:13:57 2021 +0000 +++ b/unipept.py Sat Jul 02 13:46:38 2022 +0000 |
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| @@ -486,7 +486,7 @@ parser.add_option('-T', '--tsv', dest='tsv', default=None, help='Output file path for TAB-separated-values (.tsv) formatted results') parser.add_option('-C', '--csv', dest='csv', default=None, help='Output file path for Comma-separated-values (.csv) formatted results') parser.add_option('-U', '--unmatched', dest='unmatched', default=None, help='Output file path for peptide with no matches') - parser.add_option('-u', '--url', dest='url', default='http://api.unipept.ugent.be/api/v1/', help='unipept url http://api.unipept.ugent.be/api/v1/') + parser.add_option('-u', '--url', dest='url', default='https://api.unipept.ugent.be/api/v1/', help='unipept url https://api.unipept.ugent.be/api/v1/') parser.add_option('-P', '--peptide_match', dest='peptide_match', choices=['best', 'full', 'report'], default='best', help='Match whole peptide') parser.add_option('--unmatched_aa', dest='unmatched_aa', default=None, help='Show unmatched AA in peptide as') # debug |
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| diff -r 75b3b3d0adbf -r 7863f1abcdda unipept.xml --- a/unipept.xml Tue Apr 06 16:13:57 2021 +0000 +++ b/unipept.xml Sat Jul 02 13:46:38 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="unipept" name="Unipept" version="4.5.0"> +<tool id="unipept" name="Unipept" version="4.5.1"> <description>retrieve taxonomy for peptides</description> <macros> <xml name="equate_il"> @@ -339,7 +339,7 @@ <output name="output_tsv"> <assert_contents> <has_text text="sapiens" /> - <has_text text="paniscus" /> + <has_text text="troglodytes" /> </assert_contents> </output> </test> @@ -449,7 +449,7 @@ Retrieve Uniprot and taxanomic information for trypic peptides. - Unipept API documentation - http://unipept.ugent.be/apidocs + Unipept API documentation - https://unipept.ugent.be/apidocs **Input** @@ -464,7 +464,7 @@ **Unipept APIs** - **pept2prot** - http://unipept.ugent.be/apidocs/pept2prot + **pept2prot** - https://unipept.ugent.be/apidocs/pept2prot 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. @@ -528,7 +528,7 @@ forma_id - **pept2lca** - http://unipept.ugent.be/apidocs/pept2lca + **pept2lca** - https://unipept.ugent.be/apidocs/pept2lca 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. @@ -570,7 +570,7 @@ varietas_id forma_id - **pept2ec** - http://unipept.ugent.be/apidocs/pept2ec + **pept2ec** - https://unipept.ugent.be/apidocs/pept2ec 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. @@ -583,7 +583,7 @@ name: Optional, name of the EC-number. Included when the extra parameter is set to true. - **pept2go** - http://unipept.ugent.be/apidocs/pept2go + **pept2go** - https://unipept.ugent.be/apidocs/pept2go 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. @@ -596,7 +596,7 @@ name: Optional, name of the GO-term. Included when the extra parameter is set to true. - **pept2interpro** - http://unipept.ugent.be/apidocs/pept2interpro + **pept2interpro** - https://unipept.ugent.be/apidocs/pept2interpro 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. @@ -609,7 +609,7 @@ type: Optional, type of the InterPro entry. Included when the extra parameter is set to true. name: Optional, name of the InterPro entry. Included when the extra parameter is set to true. - **pept2funct** - http://unipept.ugent.be/apidocs/pept2funct + **pept2funct** - https://unipept.ugent.be/apidocs/pept2funct 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. @@ -635,7 +635,6 @@ Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1 Article first published online: 11 FEB 2015 DOI: 10.1002/pmic.201400361 - http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400361/abstract;jsessionid=BFF1994E4C14DA73D7C907EB208AD710.f04t04 ]]></help> <citations> |