Mercurial > repos > galaxyp > unipept

annotate unipept.xml @ 0:b33376bf2290 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
author galaxyp
date Wed, 24 Oct 2018 14:45:18 -0400
parents
children b65ee881ca64
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
1 <tool id="unipept" name="Unipept" version="4.0.0">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
2 <description>retrieve taxonomy for peptides</description>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
3 <macros>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
4 <xml name="equate_il">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
7 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
8 </xml>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
9 <xml name="extra">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
10 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
11 <yield/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
12 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
13 </xml>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
14 <xml name="extra_true">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
15 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
16 <yield/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
17 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
18 </xml>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
19 <xml name="names">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
20 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names" >
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
21 <help>return the names in complete taxonomic lineage</help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
22 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
23 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields" >
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
24 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
25 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
26 </xml>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
27 <xml name="domains">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
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)">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
29 <yield/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
30 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
31 </xml>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
32 <xml name="selected_outputs">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
33 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
34 <option value="tsv" selected="true">Tabular with one line per peptide</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
35 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
36 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
37 <yield/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
38 <option value="unmatched">Unmatched peptides</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
39 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
40 </xml>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
41 </macros>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
42 <requirements>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
43 <requirement type="package" version="2.7">python</requirement>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
44 </requirements>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
45 <stdio>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
46 <exit_code range="1:" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
47 </stdio>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
48 <command><![CDATA[
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
49 python '$__tool_directory__/unipept.py'
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
50 ## --url 'http://morty.ugent.be/api/v1' -g -M 1
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
51 --api=$unipept.api
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
52 $unipept.equate_il $unipept.extra
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
53 #if $unipept.api in ['pept2lca', 'pept2taxa', 'peptinfo']:
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
54 $unipept.names $unipept.allfields
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
55 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
56 #if $unipept.api in ['pept2go', 'pept2funct', 'peptinfo']:
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
57 $unipept.domains
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
58 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
59 $strict
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
60 #if str($peptide_src.fmt) == 'proteomic':
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
61 #if $peptide_src.input.datatype.file_ext == 'fasta':
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
62 --fasta="$peptide_src.input"
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
63 #elif $peptide_src.input.datatype.file_ext == 'mzid':
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
64 --mzid="$peptide_src.input"
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
65 #elif $peptide_src.input.datatype.file_ext == 'pepxml':
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
66 --pepxml="$peptide_src.input"
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
67 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
68 #elif str($peptide_src.fmt) == 'tabular':
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
69 --tabular="$peptide_src.input_tsv"
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
70 #set $col = int(str($peptide_src.column)) - 1
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
71 --column=$col
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
72 #elif str($peptide_src.fmt) == 'fasta':
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
73 --fasta="$peptide_src.input_fasta"
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
74 #elif str($peptide_src.fmt) == 'mzid':
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
75 --mzid="$peptide_src.input_mzid"
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
76 #elif str($peptide_src.fmt) == 'pepxml':
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
77 --pepxml="$peptide_src.input_pepxml"
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
78 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
79 #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
80 --json $output_json
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
81 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
82 #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
83 --ec_json $output_ec_json
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
84 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
85 #if 'tsv' in str($selected_outputs).split(','):
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
86 --tsv $output_tsv
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
87 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
88 #if 'csv' in str($selected_outputs).split(','):
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
89 --csv $output_csv
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
90 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
91 #if 'ec_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
92 --ec_tsv $output_ec_tsv
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
93 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
94 #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
95 --go_tsv $output_go_tsv
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
96 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
97 #if 'unmatched' in str($selected_outputs).split(','):
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
98 --unmatched $output_unmatched
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
99 #end if
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
100 ]]></command>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
101 <inputs>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
102 <conditional name="unipept">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
103 <param name="api" type="select" label="Unipept application" >
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
104 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
105 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
106 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
107 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
108 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
109 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
110 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
111 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
112 <when value="pept2lca">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
113 <expand macro="equate_il" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
114 <expand macro="extra">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
115 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
116 </expand>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
117 <expand macro="names" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
118 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
119 <when value="pept2taxa">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
120 <expand macro="equate_il" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
121 <expand macro="extra_true">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
122 <help>Return the complete lineage of each organism, and include ID fields.</help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
123 </expand>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
124 <expand macro="names" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
125 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
126 <when value="pept2prot">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
127 <expand macro="equate_il" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
128 <expand macro="extra">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
129 <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
130 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
131 </help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
132 </expand>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
133 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
134 <when value="pept2ec">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
135 <expand macro="equate_il" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
136 <expand macro="extra_true">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
137 <help>Return the name of the EC-number.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
138 </help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
139 </expand>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
140 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
141 <when value="pept2go">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
142 <expand macro="equate_il" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
143 <expand macro="extra_true">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
144 <help>Return the name of the GO-term.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
145 </help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
146 </expand>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
147 <expand macro="domains" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
148 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
149 <when value="pept2funct">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
150 <expand macro="equate_il" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
151 <expand macro="extra_true">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
152 <help>Return the name of the EC-number and GO-term.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
153 </help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
154 </expand>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
155 <expand macro="domains" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
156 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
157 <when value="peptinfo">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
158 <expand macro="equate_il" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
159 <expand macro="extra_true">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
160 <help>Return the name of the EC-number and GO-term.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
161 </help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
162 </expand>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
163 <expand macro="domains" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
164 <expand macro="names" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
165 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
166 </conditional>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
167 <conditional name="peptide_src">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
168 <param name="fmt" type="select" label="Peptides input format" >
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
169 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
170 <option value="tabular">tabular</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
171 <option value="fasta">fasta</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
172 <option value="mzid">mzid</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
173 <option value="pepxml">pepxml</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
174 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
175 <when value="proteomic">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
176 <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
177 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
178 <when value="tabular">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
179 <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
180 <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
181 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
182 <when value="fasta">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
183 <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
184 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
185 <when value="mzid">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
186 <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
187 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
188 <when value="pepxml">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
189 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
190 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
191 </conditional>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
192 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
193 <option value="tsv" selected="true">Tabular with one line per peptide</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
194 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
195 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
196 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
197 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
198 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
199 <option value="unmatched">Unmatched peptides</option>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
200 </param>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
201 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
202 </inputs>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
203 <outputs>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
204 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
205 <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
206 <change_format>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
207 <when input="api" value="pept2prot" format="json" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
208 </change_format>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
209 </data>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
210 <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
211 <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
212 </data>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
213 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
214 <filter>'tsv' in selected_outputs</filter>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
215 <actions>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
216 <action name="comment_lines" type="metadata" default="1" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
217 <!--
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
218 <conditional name="unipept.api">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
219 <when value="pept2funct">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
220 <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" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
221 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
222 <when value="pept2go">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
223 <action name="column_names" type="metadata" default="peptide,total_protein_count,go_terms,go_protein_counts,go_names" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
224 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
225 <when value="pept2ec">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
226 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
227 </when>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
228 </conditional>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
229 -->
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
230 </actions>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
231 peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
232 </data>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
233 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
234 <filter>'csv' in selected_outputs</filter>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
235 </data>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
236 <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
237 <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
238 <actions>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
239 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
240 </actions>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
241 </data>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
242 <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
243 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
244 <actions>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
245 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
246 </actions>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
247 </data>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
248 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
249 <filter>'unmatched' in selected_outputs</filter>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
250 <actions>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
251 <action name="column_names" type="metadata" default="Unmatched Peptide" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
252 </actions>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
253 </data>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
254 </outputs>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
255 <tests>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
256 <test>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
257 <param name="api" value="pept2lca"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
258 <param name="fmt" value="tabular"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
259 <param name="input_tsv" value="tryptic.tsv"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
260 <param name="column" value="2"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
261 <param name="extra" value="True"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
262 <param name="names" value="True"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
263 <param name="selected_outputs" value="tsv,unmatched"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
264 <output name="output_tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
265 <assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
266 <has_text text="Homininae" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
267 </assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
268 </output>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
269 <output name="output_unmatched">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
270 <assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
271 <has_text text="QTAMAV" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
272 </assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
273 </output>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
274 </test>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
275 <test>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
276 <param name="api" value="pept2lca"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
277 <param name="fmt" value="fasta"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
278 <param name="input_fasta" value="peptide.fa"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
279 <param name="equate_il" value="True"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
280 <param name="extra" value="True"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
281 <param name="names" value="True"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
282 <param name="selected_outputs" value="json,tsv"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
283 <output name="output_json">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
284 <assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
285 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
286 </assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
287 </output>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
288 <output name="output_tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
289 <assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
290 <has_text text="9606" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
291 <has_text text="9598" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
292 </assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
293 </output>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
294 </test>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
295 <test>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
296 <param name="api" value="pept2taxa"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
297 <param name="fmt" value="fasta"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
298 <param name="input_fasta" value="peptide.fa"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
299 <param name="equate_il" value="True"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
300 <param name="extra" value="False"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
301 <param name="names" value="False"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
302 <param name="selected_outputs" value="tsv"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
303 <output name="output_tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
304 <assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
305 <has_text text="sapiens" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
306 <has_text text="troglodytes" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
307 <has_text text="Gorilla" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
308 <has_text text="Macaca" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
309 </assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
310 </output>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
311 </test>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
312 <test>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
313 <param name="api" value="pept2lca"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
314 <param name="fmt" value="tabular"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
315 <param name="input_tsv" value="tryptic.tsv"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
316 <param name="column" value="2"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
317 <param name="extra" value="True"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
318 <param name="names" value="True"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
319 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,unmatched"/>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
320 <output name="output_tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
321 <assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
322 <has_text text="3.2.1.17" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
323 </assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
324 </output>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
325 <output name="output_ec_tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
326 <assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
327 <has_text text="3.2.1.17" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
328 </assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
329 </output>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
330 <output name="output_go_tsv">
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
331 <assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
332 <has_text text="GO:0006412" />
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
333 </assert_contents>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
334 </output>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
335 </test>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
336 </tests>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
337 <help><![CDATA[
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
338 **Unipept**
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
339
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
340 Retrieve Uniprot and taxanomic information for trypic peptides.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
341
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
342 Unipept API documentation - http://unipept.ugent.be/apidocs
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
343
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
344 **Input**
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
345
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
346 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
347
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
348 Processing deatils::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
349
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
350 The input peptides are split into typtic peptide fragments in order to match the Unipept records.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
351 Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
352 The match to the most specific tryptic fragment is reported.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
353
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
354
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
355 **Unipept APIs**
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
356
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
357 **pept2prot** - http://unipept.ugent.be/apidocs/pept2prot
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
358
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
359 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.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
360
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
361 By default, each object contains the following information fields extracted from the UniProt record::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
362
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
363 peptide: the peptide that matched this record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
364 uniprot_id: the UniProt accession number of the matching record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
365 taxon_id: the NCBI taxon id of the organism associated with the matching record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
366
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
367 When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
368
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
369 taxon_name: the name of the organism associated with the matching UniProt record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
370 ec_references: a space separated list of associated EC numbers
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
371 go_references: a space separated list of associated GO terms
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
372 refseq_ids: a space separated list of associated RefSeq accession numbers
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
373 refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
374 insdc_ids: a space separated list of associated insdc accession numbers
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
375 insdc_protein_ids: a space separated list of associated insdc protein accession numbers
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
376
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
377
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
378 **pept2taxa** - http://unipept.ugent.be/apidocs/pept2taxa
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
379
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
380 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.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
381
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
382 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
383
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
384 peptide: the peptide that matched this record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
385 taxon_id: the NCBI taxon id of the organism associated with the matching record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
386 taxon_name: the name of the organism associated with the matching record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
387 taxon_rank: the taxonomic rank of the organism associated with the matching record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
388
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
389 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::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
390
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
391 superkingdom_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
392 kingdom_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
393 subkingdom_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
394 superphylum_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
395 phylum_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
396 subphylum_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
397 superclass_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
398 class_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
399 subclass_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
400 infraclass_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
401 superorder_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
402 order_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
403 suborder_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
404 infraorder_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
405 parvorder_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
406 superfamily_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
407 family_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
408 subfamily_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
409 tribe_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
410 subtribe_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
411 genus_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
412 subgenus_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
413 species_group_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
414 species_subgroup_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
415 species_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
416 subspecies_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
417 varietas_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
418 forma_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
419
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
420
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
421 **pept2lca** - http://unipept.ugent.be/apidocs/pept2lca
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
422
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
423 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.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
424
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
425 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
426
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
427 peptide: the peptide that matched this record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
428 taxon_id: the NCBI taxon id of the organism associated with the matching record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
429 taxon_name: the name of the organism associated with the matching record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
430 taxon_rank: the taxonomic rank of the organism associated with the matching record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
431
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
432 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::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
433
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
434 superkingdom_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
435 kingdom_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
436 subkingdom_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
437 superphylum_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
438 phylum_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
439 subphylum_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
440 superclass_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
441 class_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
442 subclass_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
443 infraclass_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
444 superorder_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
445 order_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
446 suborder_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
447 infraorder_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
448 parvorder_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
449 superfamily_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
450 family_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
451 subfamily_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
452 tribe_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
453 subtribe_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
454 genus_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
455 subgenus_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
456 species_group_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
457 species_subgroup_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
458 species_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
459 subspecies_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
460 varietas_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
461 forma_id
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
462
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
463 **pept2ec** - http://unipept.ugent.be/apidocs/pept2ec
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
464
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
465 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.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
466
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
467 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
468
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
469 peptide: the peptide that matched this record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
470 total_protein_count: Total amount of proteins matched with the given peptide
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
471 ec_number: EC-number associated with the current tryptic peptide.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
472 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
473 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
474
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
475
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
476 **pept2go** - http://unipept.ugent.be/apidocs/pept2go
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
477
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
478 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.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
479
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
480 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
481
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
482 peptide: the peptide that matched this record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
483 total_protein_count: Total amount of proteins matched with the given peptide
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
484 go_term: The GO-term associated with the current tryptic peptide.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
485 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
486 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
487
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
488
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
489 **pept2funct** - http://unipept.ugent.be/apidocs/pept2funct
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
490
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
491 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.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
492
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
493 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
494
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
495 peptide: the peptide that matched this record
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
496 total_protein_count: Total amount of proteins matched with the given peptide
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
497 ec_number: EC-number associated with the current tryptic peptide.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
498 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
499 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
500 go_term: The GO-term associated with the current tryptic peptide.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
501 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
502 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
503
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
504
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
505 **Attributions**
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
506
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
507 The Unipept metaproteomics analysis pipeline
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
508 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
509 Article first published online: 11 FEB 2015
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
510 DOI: 10.1002/pmic.201400361
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
511 http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400361/abstract;jsessionid=BFF1994E4C14DA73D7C907EB208AD710.f04t04
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
512
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
513 ]]></help>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
514 <citations>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
515 <citation type="doi">doi:10.1002/pmic.201400361</citation>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
516 </citations>
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
517
b33376bf2290 planemo upload for repository http://unipept.ugent.be/apidocs commit 704a0414b2547298b2596219998002491505d927-dirty
galaxyp
parents:
diff changeset
518 </tool>