unipept: unipept.xml annotate

annotate unipept.xml @ 9:21a560af5913 draft default tip

planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7

author	galaxyp
date	Tue, 12 Mar 2024 11:44:08 +0000
parents	7863f1abcdda
children

rev	line source
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	1 <tool id="unipept" name="Unipept" version="4.5.1" profile="22.05">
0 6430407e5869 Uploaded galaxyp parents: diff changeset	2 <description>retrieve taxonomy for peptides</description>
6430407e5869 Uploaded galaxyp parents: diff changeset	3 <macros>
6430407e5869 Uploaded galaxyp parents: diff changeset	4 <xml name="equate_il">
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	5 <param name="equate_il" type="boolean" truevalue="-e" falsevalue="" checked="true" label="Equate isoleucine and leucine">
0 6430407e5869 Uploaded galaxyp parents: diff changeset	6 <help>isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records</help>
3 34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	7 </param>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	8 </xml>
6430407e5869 Uploaded galaxyp parents: diff changeset	9 <xml name="extra">
6430407e5869 Uploaded galaxyp parents: diff changeset	10 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="false" label="retrieve extra information">
6430407e5869 Uploaded galaxyp parents: diff changeset	11 <yield/>
3 34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	12 </param>
34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	13 </xml>
34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	14 <xml name="extra_true">
34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	15 <param name="extra" type="boolean" truevalue="-x" falsevalue="" checked="true" label="retrieve extra information">
34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	16 <yield/>
34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	17 </param>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	18 </xml>
6430407e5869 Uploaded galaxyp parents: diff changeset	19 <xml name="names">
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	20 <param name="names" type="boolean" truevalue="-n" falsevalue="" checked="true" label="names">
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	21 <help>return the names in complete taxonomic lineage</help>
3 34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	22 </param>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	23 <param name="allfields" type="boolean" truevalue="-A" falsevalue="" checked="false" label="allfields">
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	24 <help>include fields for most specific taxonomic classification: taxon_rank,taxon_id,taxon_name before lineage</help>
3 34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	25 </param>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	26 </xml>
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	27 <xml name="domains">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	28 <param name="domains" type="boolean" truevalue="-D" falsevalue="" checked="false" label="group responses by GO namespace (biological process, molecular function, cellular component)">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	29 <yield/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	30 </param>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	31 </xml>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	32 <xml name="selected_outputs">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	33 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	34 <option value="tsv" selected="true">Tabular with one line per peptide</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	35 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	36 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	37 <yield/>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	38 <option value="unmatched">Unmatched peptides</option>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	39 </param>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	40 </xml>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	41 </macros>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	42 <xrefs>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	43 <xref type="bio.tools">unipept</xref>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	44 </xrefs>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	45 <requirements>
5 917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	46 <requirement type="package" version="3">python</requirement>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	47 </requirements>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	48 <command detect_errors="exit_code"><![CDATA[
3 34758ab8aaa4 Uploaded galaxyp parents: 2 diff changeset	49 python '$__tool_directory__/unipept.py'
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	50 ## --url 'http://morty.ugent.be/api/v1' -g -M 1
0 6430407e5869 Uploaded galaxyp parents: diff changeset	51 --api=$unipept.api
6430407e5869 Uploaded galaxyp parents: diff changeset	52 $unipept.equate_il $unipept.extra
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	53 #if $unipept.api in ['pept2lca', 'pept2taxa', 'peptinfo']:
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	54 $unipept.names $unipept.allfields
0 6430407e5869 Uploaded galaxyp parents: diff changeset	55 #end if
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	56 #if $unipept.api in ['pept2go', 'pept2funct', 'peptinfo']:
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	57 $unipept.domains
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	58 #end if
0 6430407e5869 Uploaded galaxyp parents: diff changeset	59 $strict
6430407e5869 Uploaded galaxyp parents: diff changeset	60 #if str($peptide_src.fmt) == 'proteomic':
6430407e5869 Uploaded galaxyp parents: diff changeset	61 #if $peptide_src.input.datatype.file_ext == 'fasta':
6430407e5869 Uploaded galaxyp parents: diff changeset	62 --fasta="$peptide_src.input"
6430407e5869 Uploaded galaxyp parents: diff changeset	63 #elif $peptide_src.input.datatype.file_ext == 'mzid':
6430407e5869 Uploaded galaxyp parents: diff changeset	64 --mzid="$peptide_src.input"
6430407e5869 Uploaded galaxyp parents: diff changeset	65 #elif $peptide_src.input.datatype.file_ext == 'pepxml':
6430407e5869 Uploaded galaxyp parents: diff changeset	66 --pepxml="$peptide_src.input"
6430407e5869 Uploaded galaxyp parents: diff changeset	67 #end if
6430407e5869 Uploaded galaxyp parents: diff changeset	68 #elif str($peptide_src.fmt) == 'tabular':
6430407e5869 Uploaded galaxyp parents: diff changeset	69 --tabular="$peptide_src.input_tsv"
6430407e5869 Uploaded galaxyp parents: diff changeset	70 #set $col = int(str($peptide_src.column)) - 1
6430407e5869 Uploaded galaxyp parents: diff changeset	71 --column=$col
6430407e5869 Uploaded galaxyp parents: diff changeset	72 #elif str($peptide_src.fmt) == 'fasta':
6430407e5869 Uploaded galaxyp parents: diff changeset	73 --fasta="$peptide_src.input_fasta"
6430407e5869 Uploaded galaxyp parents: diff changeset	74 #elif str($peptide_src.fmt) == 'mzid':
6430407e5869 Uploaded galaxyp parents: diff changeset	75 --mzid="$peptide_src.input_mzid"
6430407e5869 Uploaded galaxyp parents: diff changeset	76 #elif str($peptide_src.fmt) == 'pepxml':
6430407e5869 Uploaded galaxyp parents: diff changeset	77 --pepxml="$peptide_src.input_pepxml"
6430407e5869 Uploaded galaxyp parents: diff changeset	78 #end if
7 75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708" galaxyp parents: 5 diff changeset	79 --peptide_match $peptide_match
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708" galaxyp parents: 5 diff changeset	80 #if $peptide_match == 'report' and $unmatched_aa != 'default':
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708" galaxyp parents: 5 diff changeset	81 --unmatched_aa $unmatched_aa
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708" galaxyp parents: 5 diff changeset	82 #end if
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	83 #if 'json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2lca', 'pept2taxa', 'peptinfo']:
0 6430407e5869 Uploaded galaxyp parents: diff changeset	84 --json $output_json
6430407e5869 Uploaded galaxyp parents: diff changeset	85 #end if
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	86 #if 'ec_json' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	87 --ec_json $output_ec_json
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	88 #end if
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	89 #if 'tsv' in str($selected_outputs).split(','):
0 6430407e5869 Uploaded galaxyp parents: diff changeset	90 --tsv $output_tsv
6430407e5869 Uploaded galaxyp parents: diff changeset	91 #end if
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	92 #if 'csv' in str($selected_outputs).split(','):
0 6430407e5869 Uploaded galaxyp parents: diff changeset	93 --csv $output_csv
6430407e5869 Uploaded galaxyp parents: diff changeset	94 #end if
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	95 #if 'ec_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2ec', 'pept2funct', 'peptinfo']:
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	96 --ec_tsv $output_ec_tsv
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	97 #end if
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	98 #if 'go_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2go', 'pept2funct', 'peptinfo']:
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	99 --go_tsv $output_go_tsv
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	100 #end if
5 917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	101 #if 'ipr_tsv' in str($selected_outputs).split(',') and str($unipept.api) in ['pept2interpro', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	102 --ipr_tsv $output_ipr_tsv
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	103 #end if
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	104 #if 'unmatched' in str($selected_outputs).split(','):
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	105 --unmatched $output_unmatched
0 6430407e5869 Uploaded galaxyp parents: diff changeset	106 #end if
6430407e5869 Uploaded galaxyp parents: diff changeset	107 ]]></command>
6430407e5869 Uploaded galaxyp parents: diff changeset	108 <inputs>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	109 <conditional name="unipept">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	110 <param name="api" type="select" label="Unipept application">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	111 <option value="pept2lca" selected="true">pept2lca: lowest common ancestor</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	112 <option value="pept2taxa">pept2taxa: organisms associated with the UniProt entries containing a given tryptic peptide</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	113 <option value="pept2prot">pept2prot: UniProt entries containing a given tryptic peptide</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	114 <option value="pept2ec">pept2ec: Tryptic peptides and associated EC terms</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	115 <option value="pept2go">pept2go: Tryptic peptides and associated GO terms</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	116 <option value="pept2interpro">pept2interpro: Tryptic peptides and associated InterPro entries</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	117 <option value="pept2funct">pept2funct: Tryptic peptides and associated EC and GO terms</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	118 <option value="peptinfo">peptinfo: Tryptic peptides and associated EC and GO terms and lowest common ancestor taxonomy</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	119 </param>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	120 <when value="pept2lca">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	121 <expand macro="equate_il"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	122 <expand macro="extra">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	123 <help>Return the complete lineage of the taxonomic lowest common ancestor, and include ID fields.</help>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	124 </expand>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	125 <expand macro="names"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	126 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	127 <when value="pept2taxa">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	128 <expand macro="equate_il"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	129 <expand macro="extra_true">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	130 <help>Return the complete lineage of each organism, and include ID fields.</help>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	131 </expand>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	132 <expand macro="names"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	133 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	134 <when value="pept2prot">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	135 <expand macro="equate_il"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	136 <expand macro="extra">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	137 <help>Return additional information fields: taxon_name, ec_references, go_references, refseq_ids, refseq_protein_ids, insdc_ids, insdc_protein_ids
0 6430407e5869 Uploaded galaxyp parents: diff changeset	138 WARNING: Huge perfomance penalty! Only use for small number of peptides when the extra infomation is required.
6430407e5869 Uploaded galaxyp parents: diff changeset	139 </help>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	140 </expand>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	141 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	142 <when value="pept2ec">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	143 <expand macro="equate_il"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	144 <expand macro="extra_true">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	145 <help>Return the name of the EC-number.
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	146 </help>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	147 </expand>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	148 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	149 <when value="pept2go">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	150 <expand macro="equate_il"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	151 <expand macro="extra_true">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	152 <help>Return the name of the GO-term.
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	153 </help>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	154 </expand>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	155 <expand macro="domains"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	156 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	157 <when value="pept2interpro">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	158 <expand macro="equate_il"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	159 <expand macro="extra_true">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	160 <help>Return the name of the GO-term.
5 917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	161 </help>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	162 </expand>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	163 <expand macro="domains"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	164 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	165 <when value="pept2funct">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	166 <expand macro="equate_il"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	167 <expand macro="extra_true">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	168 <help>Return the name of the EC-number and GO-term.
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	169 </help>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	170 </expand>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	171 <expand macro="domains"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	172 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	173 <when value="peptinfo">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	174 <expand macro="equate_il"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	175 <expand macro="extra_true">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	176 <help>Return the name of the EC-number and GO-term.
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	177 </help>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	178 </expand>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	179 <expand macro="domains"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	180 <expand macro="names"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	181 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	182 </conditional>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	183 <conditional name="peptide_src">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	184 <param name="fmt" type="select" label="Peptides input format">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	185 <option value="proteomic">proteomics formats: mzid, pepxml, fasta</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	186 <option value="tabular">tabular</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	187 <option value="fasta">fasta</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	188 <option value="mzid">mzid</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	189 <option value="pepxml">pepxml</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	190 </param>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	191 <when value="proteomic">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	192 <param name="input" type="data" format="mzid,pepxml,fasta" label="Peptide Input"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	193 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	194 <when value="tabular">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	195 <param name="input_tsv" type="data" format="tabular" label="Tabular Input Containing Peptide column"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	196 <param name="column" label="Select column with peptides" type="data_column" numerical="false" data_ref="input_tsv"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	197 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	198 <when value="fasta">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	199 <param name="input_fasta" type="data" format="fasta" label="Peptide Fasta Input"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	200 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	201 <when value="mzid">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	202 <param name="input_mzid" type="data" format="mzid" label="mzIndetML Input"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	203 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	204 <when value="pepxml">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	205 <param name="input_pepxml" type="data" format="pepxml" label="mzIndetML Input"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	206 </when>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	207 </conditional>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	208 <param name="peptide_match" type="select" label="Match input peptides by">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	209 <option value="full">Match to the full input peptide</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	210 <option value="best" selected="true">Best match to tryptic parts of the input peptide</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	211 <option value="report">Best match to tryptic parts, add tryptic_match column</option>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	212 </param>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	213 <param name="unmatched_aa" type="select" label="Show tryptic_match as:">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	214 <option value="default">List of matched tryptic parts</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	215 <option value=".">peptide with unmatched AAs as .</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	216 <option value="x">peptide with unmatched AAs as x</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	217 </param>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	218 <param name="selected_outputs" type="select" multiple="true" display="checkboxes" label="Choose outputs">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	219 <option value="tsv" selected="true">Tabular with one line per peptide</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	220 <option value="csv">Comma Separated Values (.csv) with one line per peptide</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	221 <option value="json">JSON Taxomony Tree (for pept2lca, pep2taxa, and peptinfo)</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	222 <option value="go_tsv">Peptide GO terms in normalized tabular (for pept2go, pept2funct, and peptinfo)</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	223 <option value="ipr_tsv">Peptide InterPro entries in normalized tabular (for pept2interpro, pept2funct, and peptinfo)</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	224 <option value="ec_tsv">Peptide EC terms in normalized tabular (for pept2ec, pept2funct, and peptinfo)</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	225 <option value="ec_json">JSON EC Coverage Tree (for pept2ec, pep2funct, and peptinfo)</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	226 <option value="unmatched">Unmatched peptides</option>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	227 </param>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	228 <param name="strict" type="boolean" truevalue="--strict" falsevalue="" checked="false" label="Exit with error on invalid peptides, otherwise ignore them"/>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	229 </inputs>
6430407e5869 Uploaded galaxyp parents: diff changeset	230 <outputs>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	231 <data name="output_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} Taxonomy json">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	232 <filter>'json' in selected_outputs and unipept['api'] in ('pept2lca', 'pept2taxa', 'peptinfo')</filter>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	233 <change_format>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	234 <when input="api" value="pept2prot" format="json"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	235 </change_format>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	236 </data>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	237 <data name="output_ec_json" format="d3_hierarchy" label="${tool.name} ${unipept.api} on ${on_string} EC json">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	238 <filter>'ec_json' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	239 </data>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	240 <data name="output_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	241 <filter>'tsv' in selected_outputs</filter>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	242 <actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	243 <action name="comment_lines" type="metadata" default="1"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	244 <!--
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	245 <conditional name="unipept.api">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	246 <when value="pept2funct">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	247 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names,go_terms,go_protein_counts,go_names" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	248 </when>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	249 <when value="pept2go">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	250 <action name="column_names" type="metadata" default="peptide,total_protein_count,go_terms,go_protein_counts,go_names" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	251 </when>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	252 <when value="pept2ec">
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	253 <action name="column_names" type="metadata" default="peptide,total_protein_count,ec_numbers,ec_protein_counts,ec_names" />
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	254 </when>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	255 </conditional>
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	256 -->
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	257 </actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	258 </data>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	259 <data name="output_csv" format="csv" label="${tool.name} ${unipept.api} on ${on_string} csv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	260 <filter>'csv' in selected_outputs</filter>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	261 </data>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	262 <data name="output_ec_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} EC tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	263 <filter>'ec_tsv' in selected_outputs and unipept['api'] in ('pept2ec', 'pept2funct', 'peptinfo')</filter>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	264 <actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	265 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,EC Number,Protein Count,EC Name"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	266 </actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	267 </data>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	268 <data name="output_go_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} GO tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	269 <filter>'go_tsv' in selected_outputs and unipept['api'] in ('pept2go', 'pept2funct', 'peptinfo')</filter>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	270 <actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	271 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,GO Term,Protein Count,GO Name"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	272 </actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	273 </data>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	274 <data name="output_ipr_tsv" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} InterPro tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	275 <filter>'ipr_tsv' in selected_outputs and unipept['api'] in ('pept2interpro', 'pept2funct', 'peptinfo')</filter>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	276 <actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	277 <action name="column_names" type="metadata" default="Peptide,Total Protein Count,InterPro Code,Protein Count,InterPro Type,InterPro Name"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	278 </actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	279 </data>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	280 <data name="output_unmatched" format="tabular" label="${tool.name} ${unipept.api} on ${on_string} unmatched">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	281 <filter>'unmatched' in selected_outputs</filter>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	282 <actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	283 <action name="column_names" type="metadata" default="Unmatched Peptide"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	284 </actions>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	285 </data>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	286 </outputs>
6430407e5869 Uploaded galaxyp parents: diff changeset	287 <tests>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	288 <!-- Test-1 -->
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	289 <test expect_num_outputs="2">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	290 <param name="api" value="pept2lca"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	291 <param name="fmt" value="tabular"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	292 <param name="input_tsv" value="tryptic.tsv"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	293 <param name="column" value="2"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	294 <param name="extra" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	295 <param name="names" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	296 <param name="selected_outputs" value="tsv,unmatched"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	297 <output name="output_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	298 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	299 <has_text text="Homininae"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	300 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	301 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	302 <output name="output_unmatched">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	303 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	304 <has_text text="QTAMAV"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	305 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	306 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	307 </test>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	308 <!-- Test-2 -->
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	309 <test expect_num_outputs="2">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	310 <param name="api" value="pept2lca"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	311 <param name="fmt" value="fasta"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	312 <param name="input_fasta" value="peptide.fa"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	313 <param name="equate_il" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	314 <param name="extra" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	315 <param name="names" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	316 <param name="selected_outputs" value="json,tsv"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	317 <output name="output_json">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	318 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	319 <has_text text="VMDVNDHKPEFYNCSLPACTFTPEEAQVNFTGYVDEHASPHIPIDDLTMVVYDPDKGSNGTFLLSLGGPDAEAFSVSPERAAGSASVQVLVRVSALVDYERQTAMAV"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	320 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	321 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	322 <output name="output_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	323 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	324 <has_text text="9606"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	325 <has_text text="9596"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	326 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	327 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	328 </test>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	329 <!-- Test-3 -->
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	330 <test expect_num_outputs="1">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	331 <param name="api" value="pept2taxa"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	332 <param name="fmt" value="fasta"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	333 <param name="input_fasta" value="peptide.fa"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	334 <param name="equate_il" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	335 <param name="extra" value="False"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	336 <param name="names" value="False"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	337 <param name="selected_outputs" value="tsv"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	338 <output name="output_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	339 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	340 <has_text text="sapiens"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	341 <has_text text="Cercocebus"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	342 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	343 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	344 </test>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	345 <!-- Test-4 -->
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	346 <test expect_num_outputs="5">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	347 <param name="api" value="pept2funct"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	348 <param name="fmt" value="tabular"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	349 <param name="input_tsv" value="input.tsv"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	350 <param name="column" value="2"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	351 <param name="extra" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	352 <param name="names" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	353 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	354 <output name="output_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	355 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	356 <has_text text="GO:0004802"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	357 <has_text text="2.2.1.1"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	358 <has_text text="IPR005475"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	359 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	360 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	361 <output name="output_ec_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	362 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	363 <has_text text="2.2.1.1"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	364 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	365 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	366 <output name="output_go_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	367 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	368 <has_text text="GO:0004802"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	369 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	370 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	371 <output name="output_ipr_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	372 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	373 <has_text text="IPR005475"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	374 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	375 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	376 </test>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	377 <!-- Test-5 -->
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	378 <test expect_num_outputs="5">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	379 <param name="api" value="pept2funct"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	380 <param name="fmt" value="tabular"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	381 <param name="input_tsv" value="input.tsv"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	382 <param name="column" value="2"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	383 <param name="extra" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	384 <param name="names" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	385 <param name="peptide_match" value="full"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	386 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	387 <output name="output_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	388 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	389 <has_text text="GO:0004802"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	390 <has_text text="2.2.1.1"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	391 <has_text text="IPR005475"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	392 <has_text_matching expression="FAPLLEEYKAEDWVQK\t0"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	393 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	394 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	395 <output name="output_ec_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	396 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	397 <has_text text="2.2.1.1"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	398 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	399 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	400 <output name="output_go_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	401 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	402 <has_text text="GO:0004802"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	403 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	404 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	405 <output name="output_ipr_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	406 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	407 <has_text text="IPR005475"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	408 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	409 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	410 </test>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	411 <!-- Test-6 -->
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	412 <test expect_num_outputs="5">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	413 <param name="api" value="pept2funct"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	414 <param name="fmt" value="tabular"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	415 <param name="input_tsv" value="input.tsv"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	416 <param name="column" value="2"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	417 <param name="extra" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	418 <param name="names" value="True"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	419 <param name="peptide_match" value="report"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	420 <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	421 <output name="output_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	422 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	423 <has_text text="GO:0004802"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	424 <has_text text="2.2.1.1"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	425 <has_text text="IPR005475"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	426 <has_text_matching expression="AAEGGLSR\tAAEGGLSR\t6"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	427 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	428 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	429 <output name="output_ec_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	430 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	431 <has_text text="2.2.1.1"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	432 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	433 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	434 <output name="output_go_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	435 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	436 <has_text text="GO:0004802"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	437 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	438 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	439 <output name="output_ipr_tsv">
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	440 <assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	441 <has_text text="IPR005475"/>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	442 </assert_contents>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	443 </output>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	444 </test>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	445 </tests>
6430407e5869 Uploaded galaxyp parents: diff changeset	446 <help><![CDATA[
6430407e5869 Uploaded galaxyp parents: diff changeset	447 Unipept
6430407e5869 Uploaded galaxyp parents: diff changeset	448
6430407e5869 Uploaded galaxyp parents: diff changeset	449 Retrieve Uniprot and taxanomic information for trypic peptides.
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	450
8 7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5 galaxyp parents: 7 diff changeset	451 Unipept API documentation - https://unipept.ugent.be/apidocs
0 6430407e5869 Uploaded galaxyp parents: diff changeset	452
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	453 Input
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	454
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	455 Input peptides can be retrieved from tabular, fasta, mzid, or pepxml datasets.
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	456
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	457 Processing deatils::
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	458
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	459 The input peptides are split into typtic peptide fragments in order to match the Unipept records.
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	460 Only fragments that are complete tryptic peptides between 5 and 50 animo acid in length will be matched by Unipept.
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	461 The match to the most specific tryptic fragment is reported.
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	462
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	463
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	464 Unipept APIs
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	465
8 7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5 galaxyp parents: 7 diff changeset	466 pept2prot - https://unipept.ugent.be/apidocs/pept2prot
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	467
0 6430407e5869 Uploaded galaxyp parents: diff changeset	468 Returns the list of UniProt entries containing a given tryptic peptide. This is the same information as provided on the Protein matches tab when performing a search with the Tryptic Peptide Analysis in the web interface.
6430407e5869 Uploaded galaxyp parents: diff changeset	469
6430407e5869 Uploaded galaxyp parents: diff changeset	470 By default, each object contains the following information fields extracted from the UniProt record::
6430407e5869 Uploaded galaxyp parents: diff changeset	471
6430407e5869 Uploaded galaxyp parents: diff changeset	472 peptide: the peptide that matched this record
6430407e5869 Uploaded galaxyp parents: diff changeset	473 uniprot_id: the UniProt accession number of the matching record
6430407e5869 Uploaded galaxyp parents: diff changeset	474 taxon_id: the NCBI taxon id of the organism associated with the matching record
6430407e5869 Uploaded galaxyp parents: diff changeset	475
6430407e5869 Uploaded galaxyp parents: diff changeset	476 When the extra parameter is set to true, objects contain the following additional fields extracted from the UniProt record::
6430407e5869 Uploaded galaxyp parents: diff changeset	477
6430407e5869 Uploaded galaxyp parents: diff changeset	478 taxon_name: the name of the organism associated with the matching UniProt record
6430407e5869 Uploaded galaxyp parents: diff changeset	479 ec_references: a space separated list of associated EC numbers
6430407e5869 Uploaded galaxyp parents: diff changeset	480 go_references: a space separated list of associated GO terms
6430407e5869 Uploaded galaxyp parents: diff changeset	481 refseq_ids: a space separated list of associated RefSeq accession numbers
6430407e5869 Uploaded galaxyp parents: diff changeset	482 refseq_protein_ids: a space separated list of associated RefSeq protein accession numbers
6430407e5869 Uploaded galaxyp parents: diff changeset	483 insdc_ids: a space separated list of associated insdc accession numbers
6430407e5869 Uploaded galaxyp parents: diff changeset	484 insdc_protein_ids: a space separated list of associated insdc protein accession numbers
6430407e5869 Uploaded galaxyp parents: diff changeset	485
6430407e5869 Uploaded galaxyp parents: diff changeset	486
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	487 pept2taxa - http://unipept.ugent.be/apidocs/pept2taxa
0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	488
0 6430407e5869 Uploaded galaxyp parents: diff changeset	489 Returns the set of organisms associated with the UniProt entries containing a given tryptic peptide. This is the same information as provided on the Lineage table tab when performing a search with the Tryptic Peptide Analysis in the web interface.
6430407e5869 Uploaded galaxyp parents: diff changeset	490
6430407e5869 Uploaded galaxyp parents: diff changeset	491 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
6430407e5869 Uploaded galaxyp parents: diff changeset	492
6430407e5869 Uploaded galaxyp parents: diff changeset	493 peptide: the peptide that matched this record
6430407e5869 Uploaded galaxyp parents: diff changeset	494 taxon_id: the NCBI taxon id of the organism associated with the matching record
6430407e5869 Uploaded galaxyp parents: diff changeset	495 taxon_name: the name of the organism associated with the matching record
6430407e5869 Uploaded galaxyp parents: diff changeset	496 taxon_rank: the taxonomic rank of the organism associated with the matching record
6430407e5869 Uploaded galaxyp parents: diff changeset	497
6430407e5869 Uploaded galaxyp parents: diff changeset	498 When the extra parameter is set to true, objects contain additional information about the lineages of the organism extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields::
6430407e5869 Uploaded galaxyp parents: diff changeset	499
6430407e5869 Uploaded galaxyp parents: diff changeset	500 superkingdom_id
6430407e5869 Uploaded galaxyp parents: diff changeset	501 kingdom_id
6430407e5869 Uploaded galaxyp parents: diff changeset	502 subkingdom_id
6430407e5869 Uploaded galaxyp parents: diff changeset	503 superphylum_id
6430407e5869 Uploaded galaxyp parents: diff changeset	504 phylum_id
6430407e5869 Uploaded galaxyp parents: diff changeset	505 subphylum_id
6430407e5869 Uploaded galaxyp parents: diff changeset	506 superclass_id
6430407e5869 Uploaded galaxyp parents: diff changeset	507 class_id
6430407e5869 Uploaded galaxyp parents: diff changeset	508 subclass_id
6430407e5869 Uploaded galaxyp parents: diff changeset	509 infraclass_id
6430407e5869 Uploaded galaxyp parents: diff changeset	510 superorder_id
6430407e5869 Uploaded galaxyp parents: diff changeset	511 order_id
6430407e5869 Uploaded galaxyp parents: diff changeset	512 suborder_id
6430407e5869 Uploaded galaxyp parents: diff changeset	513 infraorder_id
6430407e5869 Uploaded galaxyp parents: diff changeset	514 parvorder_id
6430407e5869 Uploaded galaxyp parents: diff changeset	515 superfamily_id
6430407e5869 Uploaded galaxyp parents: diff changeset	516 family_id
6430407e5869 Uploaded galaxyp parents: diff changeset	517 subfamily_id
6430407e5869 Uploaded galaxyp parents: diff changeset	518 tribe_id
6430407e5869 Uploaded galaxyp parents: diff changeset	519 subtribe_id
6430407e5869 Uploaded galaxyp parents: diff changeset	520 genus_id
6430407e5869 Uploaded galaxyp parents: diff changeset	521 subgenus_id
6430407e5869 Uploaded galaxyp parents: diff changeset	522 species_group_id
6430407e5869 Uploaded galaxyp parents: diff changeset	523 species_subgroup_id
6430407e5869 Uploaded galaxyp parents: diff changeset	524 species_id
6430407e5869 Uploaded galaxyp parents: diff changeset	525 subspecies_id
6430407e5869 Uploaded galaxyp parents: diff changeset	526 varietas_id
6430407e5869 Uploaded galaxyp parents: diff changeset	527 forma_id
6430407e5869 Uploaded galaxyp parents: diff changeset	528
6430407e5869 Uploaded galaxyp parents: diff changeset	529
8 7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5 galaxyp parents: 7 diff changeset	530 pept2lca - https://unipept.ugent.be/apidocs/pept2lca
1 0c1ee95282fa Uploaded galaxyp parents: 0 diff changeset	531
0 6430407e5869 Uploaded galaxyp parents: diff changeset	532 Returns the taxonomic lowest common ancestor for a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
6430407e5869 Uploaded galaxyp parents: diff changeset	533
6430407e5869 Uploaded galaxyp parents: diff changeset	534 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
6430407e5869 Uploaded galaxyp parents: diff changeset	535
6430407e5869 Uploaded galaxyp parents: diff changeset	536 peptide: the peptide that matched this record
6430407e5869 Uploaded galaxyp parents: diff changeset	537 taxon_id: the NCBI taxon id of the organism associated with the matching record
6430407e5869 Uploaded galaxyp parents: diff changeset	538 taxon_name: the name of the organism associated with the matching record
6430407e5869 Uploaded galaxyp parents: diff changeset	539 taxon_rank: the taxonomic rank of the organism associated with the matching record
6430407e5869 Uploaded galaxyp parents: diff changeset	540
6430407e5869 Uploaded galaxyp parents: diff changeset	541 When the extra parameter is set to true, objects contain additional information about the lineage of the taxonomic lowest common ancestor extracted from the NCBI taxonomy. The taxon id of each rank in the lineage is specified using the following information fields::
6430407e5869 Uploaded galaxyp parents: diff changeset	542
6430407e5869 Uploaded galaxyp parents: diff changeset	543 superkingdom_id
6430407e5869 Uploaded galaxyp parents: diff changeset	544 kingdom_id
6430407e5869 Uploaded galaxyp parents: diff changeset	545 subkingdom_id
6430407e5869 Uploaded galaxyp parents: diff changeset	546 superphylum_id
6430407e5869 Uploaded galaxyp parents: diff changeset	547 phylum_id
6430407e5869 Uploaded galaxyp parents: diff changeset	548 subphylum_id
6430407e5869 Uploaded galaxyp parents: diff changeset	549 superclass_id
6430407e5869 Uploaded galaxyp parents: diff changeset	550 class_id
6430407e5869 Uploaded galaxyp parents: diff changeset	551 subclass_id
6430407e5869 Uploaded galaxyp parents: diff changeset	552 infraclass_id
6430407e5869 Uploaded galaxyp parents: diff changeset	553 superorder_id
6430407e5869 Uploaded galaxyp parents: diff changeset	554 order_id
6430407e5869 Uploaded galaxyp parents: diff changeset	555 suborder_id
6430407e5869 Uploaded galaxyp parents: diff changeset	556 infraorder_id
6430407e5869 Uploaded galaxyp parents: diff changeset	557 parvorder_id
6430407e5869 Uploaded galaxyp parents: diff changeset	558 superfamily_id
6430407e5869 Uploaded galaxyp parents: diff changeset	559 family_id
6430407e5869 Uploaded galaxyp parents: diff changeset	560 subfamily_id
6430407e5869 Uploaded galaxyp parents: diff changeset	561 tribe_id
6430407e5869 Uploaded galaxyp parents: diff changeset	562 subtribe_id
6430407e5869 Uploaded galaxyp parents: diff changeset	563 genus_id
6430407e5869 Uploaded galaxyp parents: diff changeset	564 subgenus_id
6430407e5869 Uploaded galaxyp parents: diff changeset	565 species_group_id
6430407e5869 Uploaded galaxyp parents: diff changeset	566 species_subgroup_id
6430407e5869 Uploaded galaxyp parents: diff changeset	567 species_id
6430407e5869 Uploaded galaxyp parents: diff changeset	568 subspecies_id
6430407e5869 Uploaded galaxyp parents: diff changeset	569 varietas_id
6430407e5869 Uploaded galaxyp parents: diff changeset	570 forma_id
6430407e5869 Uploaded galaxyp parents: diff changeset	571
8 7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5 galaxyp parents: 7 diff changeset	572 pept2ec - https://unipept.ugent.be/apidocs/pept2ec
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	573
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	574 Returns the functional EC-numbers associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	575
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	576 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	577
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	578 peptide: the peptide that matched this record
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	579 total_protein_count: Total amount of proteins matched with the given peptide
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	580 ec_number: EC-number associated with the current tryptic peptide.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	581 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	582 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	583
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	584
8 7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5 galaxyp parents: 7 diff changeset	585 pept2go - https://unipept.ugent.be/apidocs/pept2go
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	586
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	587 Returns the functional GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	588
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	589 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	590
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	591 peptide: the peptide that matched this record
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	592 total_protein_count: Total amount of proteins matched with the given peptide
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	593 go_term: The GO-term associated with the current tryptic peptide.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	594 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	595 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	596
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	597
8 7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5 galaxyp parents: 7 diff changeset	598 pept2interpro - https://unipept.ugent.be/apidocs/pept2interpro
5 917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	599
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	600 Returns the functional InterPro entries associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	601
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	602 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	603
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	604 peptide: the peptide that matched this record
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	605 total_protein_count: Total amount of proteins matched with the given peptide
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	606 code: InterPro entry code associated with the current tryptic peptide
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	607 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	608 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	609 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	610
8 7863f1abcdda planemo upload for repository https://unipept.ugent.be/apidocs commit 8b14b02c5b11232c0c2cc278e3ac492455f2e0a5 galaxyp parents: 7 diff changeset	611 pept2funct - https://unipept.ugent.be/apidocs/pept2funct
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	612
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	613 Returns the functional EC-numbers and GO-terms associated with a given tryptic peptide. This is the same information as provided when performing a search with the Tryptic Peptide Analysis in the web interface.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	614
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	615 By default, each object contains the following information fields extracted from the UniProt record and NCBI taxonomy::
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	616
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	617 peptide: the peptide that matched this record
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	618 total_protein_count: Total amount of proteins matched with the given peptide
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	619 ec_number: EC-number associated with the current tryptic peptide.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	620 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current EC-number.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	621 name: Optional, name of the EC-number. Included when the extra parameter is set to true.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	622 go_term: The GO-term associated with the current tryptic peptide.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	623 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current GO-term.
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	624 name: Optional, name of the GO-term. Included when the extra parameter is set to true.
5 917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	625 code: InterPro entry code associated with the current tryptic peptide
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	626 protein_count: amount of proteins matched with the given tryptic peptide that are labeled with the current InterPro code.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	627 type: Optional, type of the InterPro entry. Included when the extra parameter is set to true.
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty" galaxyp parents: 4 diff changeset	628 name: Optional, name of the InterPro entry. Included when the extra parameter is set to true.
4 4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty galaxyp parents: 3 diff changeset	629
0 6430407e5869 Uploaded galaxyp parents: diff changeset	630
6430407e5869 Uploaded galaxyp parents: diff changeset	631 Attributions
6430407e5869 Uploaded galaxyp parents: diff changeset	632
6430407e5869 Uploaded galaxyp parents: diff changeset	633 The Unipept metaproteomics analysis pipeline
6430407e5869 Uploaded galaxyp parents: diff changeset	634 Bart Mesuere1,*, Griet Debyser2, Maarten Aerts3, Bart Devreese2, Peter Vandamme3 andPeter Dawyndt1
6430407e5869 Uploaded galaxyp parents: diff changeset	635 Article first published online: 11 FEB 2015
6430407e5869 Uploaded galaxyp parents: diff changeset	636 DOI: 10.1002/pmic.201400361
6430407e5869 Uploaded galaxyp parents: diff changeset	637
6430407e5869 Uploaded galaxyp parents: diff changeset	638 ]]></help>
9 21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	639 <citations>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	640 <citation type="doi">doi:10.1002/pmic.201400361</citation>
21a560af5913 planemo upload for repository https://unipept.ugent.be/apidocs commit 19735e85caae264d98562f6fdb3b213841087fc7 galaxyp parents: 8 diff changeset	641 </citations>
0 6430407e5869 Uploaded galaxyp parents: diff changeset	642 </tool>

Mercurial > repos > galaxyp > unipept

annotate unipept.xml @ 9:21a560af5913 draft default tip