annotate unipept.xml @ 8:7863f1abcdda draft

planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
author galaxyp
date Sat, 02 Jul 2022 13:46:38 +0000
parents 75b3b3d0adbf
children 21a560af5913
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
1 <tool id="unipept" name="Unipept" version="4.5.1">
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
2 <description>retrieve taxonomy for peptides</description>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
3 <macros>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
4 <xml name="equate_il">
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
3
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
7 </param>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
8 </xml>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
9 <xml name="extra">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
10 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
11 <yield/>
3
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
12 </param>
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
13 </xml>
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
14 <xml name="extra_true">
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
15 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
16 <yield/>
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
17 </param>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
18 </xml>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
19 <xml name="names">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
20 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
21 <help>return the names in complete taxonomic lineage</help>
3
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
22 </param>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
23 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
24 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
3
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
25 </param>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
26 </xml>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
27 <xml name="domains">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
28 <param name="domains" type="boolean" truevalue="-D" falsevalue="" checked="false" label="group responses by GO namespace (biological process, molecular function, cellular component)">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
29 <yield/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
30 </param>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
31 </xml>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
32 <xml name="selected_outputs">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
33 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
34 <option value="tsv" selected="true">Tabular with one line per peptide</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
35 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
36 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
37 <yield/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
38 <option value="unmatched">Unmatched peptides</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
39 </param>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
40 </xml>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
41 </macros>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
42 <requirements>
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
43 <requirement type="package" version="3">python</requirement>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
44 </requirements>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
45 <stdio>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
46 <exit_code range="1:" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
47 </stdio>
3
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
48 <command><![CDATA[
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
49 python '$__tool_directory__/unipept.py'
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
50 ## --url 'http://morty.ugent.be/api/v1' -g -M 1
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
51 --api=$unipept.api
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
52 $unipept.equate_il $unipept.extra
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
53 #if $unipept.api in ['pept2lca', 'pept2taxa', 'peptinfo']:
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
54 $unipept.names $unipept.allfields
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
55 #end if
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
56 #if $unipept.api in ['pept2go', 'pept2funct', 'peptinfo']:
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
57 $unipept.domains
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
58 #end if
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
59 $strict
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
60 #if str($peptide_src.fmt) == 'proteomic':
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
61 #if $peptide_src.input.datatype.file_ext == 'fasta':
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
62 --fasta="$peptide_src.input"
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
63 #elif $peptide_src.input.datatype.file_ext == 'mzid':
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
64 --mzid="$peptide_src.input"
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
65 #elif $peptide_src.input.datatype.file_ext == 'pepxml':
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
66 --pepxml="$peptide_src.input"
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
67 #end if
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
68 #elif str($peptide_src.fmt) == 'tabular':
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
69 --tabular="$peptide_src.input_tsv"
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
70 #set $col = int(str($peptide_src.column)) - 1
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
71 --column=$col
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
72 #elif str($peptide_src.fmt) == 'fasta':
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
73 --fasta="$peptide_src.input_fasta"
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
74 #elif str($peptide_src.fmt) == 'mzid':
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
75 --mzid="$peptide_src.input_mzid"
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
76 #elif str($peptide_src.fmt) == 'pepxml':
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
77 --pepxml="$peptide_src.input_pepxml"
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
78 #end if
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
79 --peptide_match $peptide_match
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
80 #if $peptide_match == 'report' and $unmatched_aa != 'default':
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
81 --unmatched_aa $unmatched_aa
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
82 #end if
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
83 #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
84 --json $output_json
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
85 #end if
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
86 #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
87 --ec_json $output_ec_json
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
88 #end if
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
89 #if 'tsv' in str($selected_outputs).split(','):
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
90 --tsv $output_tsv
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
91 #end if
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
92 #if 'csv' in str($selected_outputs).split(','):
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
93 --csv $output_csv
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
94 #end if
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
95 #if 'ec_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
96 --ec_tsv $output_ec_tsv
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
97 #end if
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
98 #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
99 --go_tsv $output_go_tsv
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
100 #end if
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
101 #if 'ipr_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2interpro', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
102 --ipr_tsv $output_ipr_tsv
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
103 #end if
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
104 #if 'unmatched' in str($selected_outputs).split(','):
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
105 --unmatched $output_unmatched
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
106 #end if
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
107 ]]></command>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
108 <inputs>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
109 <conditional name="unipept">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
110 <param name="api" type="select" label="Unipept application" >
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
111 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
112 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
113 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
114 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
115 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
116 <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
117 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
118 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
119 </param>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
120 <when value="pept2lca">
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
121 <expand macro="equate_il" />
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
122 <expand macro="extra">
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
123 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
124 </expand>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
125 <expand macro="names" />
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
126 </when>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
127 <when value="pept2taxa">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
128 <expand macro="equate_il" />
3
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
129 <expand macro="extra_true">
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
130 <help>Return the complete lineage of each organism, and include ID fields.</help>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
131 </expand>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
132 <expand macro="names" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
133 </when>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
134 <when value="pept2prot">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
135 <expand macro="equate_il" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
136 <expand macro="extra">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
137 <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
138 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required.
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
139 </help>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
140 </expand>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
141 </when>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
142 <when value="pept2ec">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
143 <expand macro="equate_il" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
144 <expand macro="extra_true">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
145 <help>Return the name of the EC-number.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
146 </help>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
147 </expand>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
148 </when>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
149 <when value="pept2go">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
150 <expand macro="equate_il" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
151 <expand macro="extra_true">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
152 <help>Return the name of the GO-term.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
153 </help>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
154 </expand>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
155 <expand macro="domains" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
156 </when>
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
157 <when value="pept2interpro">
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
158 <expand macro="equate_il" />
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
159 <expand macro="extra_true">
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
160 <help>Return the name of the GO-term.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
161 </help>
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
162 </expand>
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
163 <expand macro="domains" />
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
164 </when>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
165 <when value="pept2funct">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
166 <expand macro="equate_il" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
167 <expand macro="extra_true">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
168 <help>Return the name of the EC-number and GO-term.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
169 </help>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
170 </expand>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
171 <expand macro="domains" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
172 </when>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
173 <when value="peptinfo">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
174 <expand macro="equate_il" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
175 <expand macro="extra_true">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
176 <help>Return the name of the EC-number and GO-term.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
177 </help>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
178 </expand>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
179 <expand macro="domains" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
180 <expand macro="names" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
181 </when>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
182 </conditional>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
183 <conditional name="peptide_src">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
184 <param name="fmt" type="select" label="Peptides input format" >
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
185 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
186 <option value="tabular">tabular</option>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
187 <option value="fasta">fasta</option>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
188 <option value="mzid">mzid</option>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
189 <option value="pepxml">pepxml</option>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
190 </param>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
191 <when value="proteomic">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
192 <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
193 </when>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
194 <when value="tabular">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
195 <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
196 <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
197 </when>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
198 <when value="fasta">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
199 <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
200 </when>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
201 <when value="mzid">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
202 <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
203 </when>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
204 <when value="pepxml">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
205 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
206 </when>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
207 </conditional>
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
208 <param name="peptide_match" type="select" label="Match input peptides by">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
209 <option value="full">Match to the full input peptide</option>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
210 <option value="best" selected="true">Best match to tryptic parts of the input peptide</option>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
211 <option value="report">Best match to tryptic parts, add tryptic_match column</option>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
212 </param>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
213 <param name="unmatched_aa" type="select" label="Show tryptic_match as:">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
214 <option value="default">List of matched tryptic parts</option>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
215 <option value=".">peptide with unmatched AAs as .</option>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
216 <option value="x">peptide with unmatched AAs as x</option>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
217 </param>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
218 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
219 <option value="tsv" selected="true">Tabular with one line per peptide</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
220 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
221 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
222 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
223 <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
224 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
225 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
226 <option value="unmatched">Unmatched peptides</option>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
227 </param>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
228 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
229 </inputs>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
230 <outputs>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
231 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
232 <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
3
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
233 <change_format>
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
234 <when input="api" value="pept2prot" format="json" />
34758ab8aaa4 Uploaded
galaxyp
parents: 2
diff changeset
235 </change_format>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
236 </data>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
237 <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
238 <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
239 </data>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
240 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
241 <filter>'tsv' in selected_outputs</filter>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
242 <actions>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
243 <action name="comment_lines" type="metadata" default="1" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
244 <!--
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
245 <conditional name="unipept.api">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
246 <when value="pept2funct">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
247 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
248 </when>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
249 <when value="pept2go">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
250 <action name="column_names" type="metadata" default="peptide,total_protein_count,go_terms,go_protein_counts,go_names" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
251 </when>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
252 <when value="pept2ec">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
253 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
254 </when>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
255 </conditional>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
256 -->
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
257 </actions>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
258 </data>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
259 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
260 <filter>'csv' in selected_outputs</filter>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
261 </data>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
262 <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
263 <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
264 <actions>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
265 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
266 </actions>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
267 </data>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
268 <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
269 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
270 <actions>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
271 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
272 </actions>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
273 </data>
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
274 <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv">
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
275 <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter>
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
276 <actions>
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
277 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name" />
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
278 </actions>
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
279 </data>
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
280
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
281 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
282 <filter>'unmatched' in selected_outputs</filter>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
283 <actions>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
284 <action name="column_names" type="metadata" default="Unmatched Peptide" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
285 </actions>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
286 </data>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
287 </outputs>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
288 <tests>
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
289 <!-- Test-1 -->
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
290 <test>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
291 <param name="api" value="pept2lca"/>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
292 <param name="fmt" value="tabular"/>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
293 <param name="input_tsv" value="tryptic.tsv"/>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
294 <param name="column" value="2"/>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
295 <param name="extra" value="True"/>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
296 <param name="names" value="True"/>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
297 <param name="selected_outputs" value="tsv,unmatched"/>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
298 <output name="output_tsv">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
299 <assert_contents>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
300 <has_text text="Homininae" />
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
301 </assert_contents>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
302 </output>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
303 <output name="output_unmatched">
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
304 <assert_contents>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
305 <has_text text="QTAMAV" />
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
306 </assert_contents>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
307 </output>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
308 </test>
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
309 <!-- Test-2 -->
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
310 <test>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
311 <param name="api" value="pept2lca"/>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
312 <param name="fmt" value="fasta"/>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
313 <param name="input_fasta" value="peptide.fa"/>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
314 <param name="equate_il" value="True"/>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
315 <param name="extra" value="True"/>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
316 <param name="names" value="True"/>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
317 <param name="selected_outputs" value="json,tsv"/>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
318 <output name="output_json">
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
319 <assert_contents>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
320 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
321 </assert_contents>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
322 </output>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
323 <output name="output_tsv">
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
324 <assert_contents>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
325 <has_text text="9606" />
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
326 <has_text text="9596" />
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
327 </assert_contents>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
328 </output>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
329 </test>
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
330 <!-- Test-3 -->
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
331 <test>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
332 <param name="api" value="pept2taxa"/>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
333 <param name="fmt" value="fasta"/>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
334 <param name="input_fasta" value="peptide.fa"/>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
335 <param name="equate_il" value="True"/>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
336 <param name="extra" value="False"/>
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
337 <param name="names" value="False"/>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
338 <param name="selected_outputs" value="tsv"/>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
339 <output name="output_tsv">
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
340 <assert_contents>
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
341 <has_text text="sapiens" />
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
342 <has_text text="troglodytes" />
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
343 </assert_contents>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
344 </output>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
345 </test>
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
346 <!-- Test-4 -->
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
347 <test>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
348 <param name="api" value="pept2funct"/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
349 <param name="fmt" value="tabular"/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
350 <param name="input_tsv" value="input.tsv"/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
351 <param name="column" value="2"/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
352 <param name="extra" value="True"/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
353 <param name="names" value="True"/>
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
354 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
355 <output name="output_tsv">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
356 <assert_contents>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
357 <has_text text="GO:0004802" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
358 <has_text text="2.2.1.1" />
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
359 <has_text text="IPR005475" />
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
360 </assert_contents>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
361 </output>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
362 <output name="output_ec_tsv">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
363 <assert_contents>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
364 <has_text text="2.2.1.1" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
365 </assert_contents>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
366 </output>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
367 <output name="output_go_tsv">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
368 <assert_contents>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
369 <has_text text="GO:0004802" />
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
370 </assert_contents>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
371 </output>
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
372 <output name="output_ipr_tsv">
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
373 <assert_contents>
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
374 <has_text text="IPR005475" />
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
375 </assert_contents>
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
376 </output>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
377 </test>
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
378 <!-- Test-5 -->
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
379 <test>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
380 <param name="api" value="pept2funct"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
381 <param name="fmt" value="tabular"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
382 <param name="input_tsv" value="input.tsv"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
383 <param name="column" value="2"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
384 <param name="extra" value="True"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
385 <param name="names" value="True"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
386 <param name="peptide_match" value="full"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
387 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
388 <output name="output_tsv">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
389 <assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
390 <has_text text="GO:0004802" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
391 <has_text text="2.2.1.1" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
392 <has_text text="IPR005475" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
393 <has_text_matching expression="FAPLLEEYKAEDWVQK\t0" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
394 </assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
395 </output>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
396 <output name="output_ec_tsv">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
397 <assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
398 <has_text text="2.2.1.1" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
399 </assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
400 </output>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
401 <output name="output_go_tsv">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
402 <assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
403 <has_text text="GO:0004802" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
404 </assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
405 </output>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
406 <output name="output_ipr_tsv">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
407 <assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
408 <has_text text="IPR005475" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
409 </assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
410 </output>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
411 </test>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
412 <!-- Test-6 -->
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
413 <test>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
414 <param name="api" value="pept2funct"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
415 <param name="fmt" value="tabular"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
416 <param name="input_tsv" value="input.tsv"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
417 <param name="column" value="2"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
418 <param name="extra" value="True"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
419 <param name="names" value="True"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
420 <param name="peptide_match" value="report"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
421 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
422 <output name="output_tsv">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
423 <assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
424 <has_text text="GO:0004802" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
425 <has_text text="2.2.1.1" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
426 <has_text text="IPR005475" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
427 <has_text_matching expression="FAPLLEEYKAEDWVQK\tAEDWVQK\t1" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
428 </assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
429 </output>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
430 <output name="output_ec_tsv">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
431 <assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
432 <has_text text="2.2.1.1" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
433 </assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
434 </output>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
435 <output name="output_go_tsv">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
436 <assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
437 <has_text text="GO:0004802" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
438 </assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
439 </output>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
440 <output name="output_ipr_tsv">
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
441 <assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
442 <has_text text="IPR005475" />
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
443 </assert_contents>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
444 </output>
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 5
diff changeset
445 </test>
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
446 </tests>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
447 <help><![CDATA[
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
448 **Unipept**
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
449
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
450 Retrieve Uniprot and taxanomic information for trypic peptides.
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
451
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
452 Unipept API documentation - https://unipept.ugent.be/apidocs
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
453
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
454 **Input**
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
455
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
456 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
457
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
458 Processing deatils::
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
459
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
460 The input peptides are split into typtic peptide fragments in order to match the Unipept records.
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
461 Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept.
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
462 The match to the most specific tryptic fragment is reported.
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
463
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
464
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
465 **Unipept APIs**
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
466
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
467 **pept2prot** - https://unipept.ugent.be/apidocs/pept2prot
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
468
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
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.
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
470
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
471 By default, each object contains the following information fields extracted from the UniProt record::
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
472
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
473 peptide: the peptide that matched this record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
474 uniprot_id: the UniProt accession number of the matching record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
475 taxon_id: the NCBI taxon id of the organism associated with the matching record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
476
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
477 When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record::
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
478
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
479 taxon_name: the name of the organism associated with the matching UniProt record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
480 ec_references: a space separated list of associated EC numbers
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
481 go_references: a space separated list of associated GO terms
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
482 refseq_ids: a space separated list of associated RefSeq accession numbers
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
483 refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
484 insdc_ids: a space separated list of associated insdc accession numbers
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
485 insdc_protein_ids: a space separated list of associated insdc protein accession numbers
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
486
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
487
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
488 **pept2taxa** - http://unipept.ugent.be/apidocs/pept2taxa
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
489
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
490 Returns the set of organisms associated with the UniProt entries containing a given tryptic peptide. This is the same information as provided on the Lineage table tab when performing a search with the Tryptic Peptide Analysis in the web interface.
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
491
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
492 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
493
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
494 peptide: the peptide that matched this record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
495 taxon_id: the NCBI taxon id of the organism associated with the matching record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
496 taxon_name: the name of the organism associated with the matching record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
497 taxon_rank: the taxonomic rank of the organism associated with the matching record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
498
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
499 When the extra parameter is set to true, objects contain additional information about the lineages of the organism extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields::
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
500
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
501 superkingdom_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
502 kingdom_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
503 subkingdom_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
504 superphylum_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
505 phylum_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
506 subphylum_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
507 superclass_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
508 class_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
509 subclass_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
510 infraclass_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
511 superorder_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
512 order_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
513 suborder_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
514 infraorder_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
515 parvorder_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
516 superfamily_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
517 family_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
518 subfamily_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
519 tribe_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
520 subtribe_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
521 genus_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
522 subgenus_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
523 species_group_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
524 species_subgroup_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
525 species_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
526 subspecies_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
527 varietas_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
528 forma_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
529
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
530
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
531 **pept2lca** - https://unipept.ugent.be/apidocs/pept2lca
1
0c1ee95282fa Uploaded
galaxyp
parents: 0
diff changeset
532
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
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.
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
534
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
535 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
536
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
537 peptide: the peptide that matched this record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
538 taxon_id: the NCBI taxon id of the organism associated with the matching record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
539 taxon_name: the name of the organism associated with the matching record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
540 taxon_rank: the taxonomic rank of the organism associated with the matching record
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
541
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
542 When the extra parameter is set to true, objects contain additional information about the lineage of the taxonomic lowest common ancestor extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields::
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
543
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
544 superkingdom_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
545 kingdom_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
546 subkingdom_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
547 superphylum_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
548 phylum_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
549 subphylum_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
550 superclass_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
551 class_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
552 subclass_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
553 infraclass_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
554 superorder_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
555 order_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
556 suborder_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
557 infraorder_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
558 parvorder_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
559 superfamily_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
560 family_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
561 subfamily_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
562 tribe_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
563 subtribe_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
564 genus_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
565 subgenus_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
566 species_group_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
567 species_subgroup_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
568 species_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
569 subspecies_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
570 varietas_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
571 forma_id
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
572
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
573 **pept2ec** - https://unipept.ugent.be/apidocs/pept2ec
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
574
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
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.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
576
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
577 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
578
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
579 peptide: the peptide that matched this record
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
580 total_protein_count: Total amount of proteins matched with the given peptide
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
581 ec_number: EC-number associated with the current tryptic peptide.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
582 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
583 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
584
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
585
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
586 **pept2go** - https://unipept.ugent.be/apidocs/pept2go
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
587
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
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.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
589
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
590 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
591
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
592 peptide: the peptide that matched this record
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
593 total_protein_count: Total amount of proteins matched with the given peptide
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
594 go_term: The GO-term associated with the current tryptic peptide.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
595 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
596 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
597
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
598
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
599 **pept2interpro** - https://unipept.ugent.be/apidocs/pept2interpro
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
600
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
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.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
602
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
603 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
604
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
605 peptide: the peptide that matched this record
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
606 total_protein_count: Total amount of proteins matched with the given peptide
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
607 code: InterPro entry code associated with the current tryptic peptide
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
608 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
609 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
610 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
611
8
7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5
galaxyp
parents: 7
diff changeset
612 **pept2funct** - https://unipept.ugent.be/apidocs/pept2funct
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
613
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
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.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
615
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
616 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
617
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
618 peptide: the peptide that matched this record
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
619 total_protein_count: Total amount of proteins matched with the given peptide
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
620 ec_number: EC-number associated with the current tryptic peptide.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
621 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
622 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
623 go_term: The GO-term associated with the current tryptic peptide.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
624 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
625 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
626 code: InterPro entry code associated with the current tryptic peptide
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
627 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
628 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
629 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
630
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
631
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
632 **Attributions**
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
633
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
634 The Unipept metaproteomics analysis pipeline
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
635 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
636 Article first published online: 11 FEB 2015
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
637 DOI: 10.1002/pmic.201400361
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
638
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
639 ]]></help>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
640 <citations>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
641 <citation type="doi">doi:10.1002/pmic.201400361</citation>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
642 </citations>
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
643
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
644 </tool>