# HG changeset patch
# User galaxyp
# Date 1656769562 0
# Node ID 42bc03ed02f6ead4fd6a156c5b78350230f107de
# Parent  1137ffa5e4796069025e570d0833fe17c5de7a58
planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5

diff -r 1137ffa5e479 -r 42bc03ed02f6 unipept.py
--- a/unipept.py	Tue Apr 06 16:13:31 2021 +0000
+++ b/unipept.py	Sat Jul 02 13:46:02 2022 +0000
@@ -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
diff -r 1137ffa5e479 -r 42bc03ed02f6 unipept.xml
--- a/unipept.xml	Tue Apr 06 16:13:31 2021 +0000
+++ b/unipept.xml	Sat Jul 02 13:46:02 2022 +0000
@@ -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>