Mercurial > repos > iuc > kobas

annotate kobas_annotate.xml @ 0:e3308a2b63f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
author iuc
date Fri, 04 Nov 2016 15:42:18 -0400
parents
children dc84c4e1f9c4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
1 <tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@">
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
2 <description>KEGG Orthology Based Annotation System</description>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
3 <macros>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
4 <import>kobas_macros.xml</import>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
5 </macros>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
6 <requirements>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
7 <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
8 </requirements>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
9 <stdio>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
10 <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
11 <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
12 </stdio>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
13 <command>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
14 <![CDATA[
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
15
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
16 ## create the KOBAS directories
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
17 mkdir sqlite &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
18 mkdir seq_pep &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
19
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
20 #if $blast_opts.choice == 'local':
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
21 #set $blast_path = $blast_opts.localdb.fields.path
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
22 #else if $blast_opts.choice == 'fasta':
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
23 makeblastdb
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
24 -in '$blast_opts.fastadb'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
25 -dbtype 'prot'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
26 -out 'seq_pep/${species}.pep.fasta' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
27 #else:
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
28 #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,'blastdb')
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
29 #end if
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
30
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
31 ## create the database symlinks to comply with how KOBAS wants them
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
32 ln -s '$organismdb' sqlite/organism.db &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
33 ln -s '$kobasdb' 'sqlite/${species}.db' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
34
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
35 #if $blast_opts.choice != 'fasta':
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
36 ln -s '${blast_path}.phr' 'seq_pep/${species}.pep.fasta.phr' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
37 ln -s '${blast_path}.pin' 'seq_pep/${species}.pep.fasta.pin' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
38 ln -s '${blast_path}.psq' 'seq_pep/${species}.pep.fasta.psq' && ls -l seq_pep/ &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
39 #end if
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
40
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
41 ## create the orthologe database symlinks to comply with how KOBAS wants them
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
42 #if $ortholog.only == 'YES' and str($ortholog.species) != str($species):
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
43
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
44 #if $ortholog.blast_opts_ortholog.choice == 'local':
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
45 #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
46 #else if $ortholog.blast_opts_ortholog.choice == 'fasta':
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
47 makeblastdb
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
48 -in '$ortholog.blast_opts_ortholog.fastadb'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
49 -dbtype 'prot'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
50 -out 'seq_pep/${ortholog.species}.pep.fasta' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
51 #else:
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
52 #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,'blastdb')
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
53 #end if
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
54
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
55 ln -s '$ortholog.kobasdb' 'sqlite/${ortholog.species}.db' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
56
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
57 #if $blast_opts.choice != 'fasta':
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
58 ln -s '${blast_path}.phr' 'seq_pep/${ortholog.species}.pep.fasta.phr' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
59 ln -s '${blast_path}.pin' 'seq_pep/${ortholog.species}.pep.fasta.pin' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
60 ln -s '${blast_path}.psq' 'seq_pep/${ortholog.species}.pep.fasta.psq' &&
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
61 #end if
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
62 #end if
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
63
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
64 kobas-annotate
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
65 -i '$infile'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
66 -t '$intype'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
67 -s '$species'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
68 -e '$evalue'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
69 -r $rank
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
70 -c $coverage
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
71 #if $ortholog.only == 'YES':
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
72 -z '$ortholog.species'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
73 #end if
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
74 -y seq_pep
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
75 -q sqlite
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
76 -p blastp
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
77 -x blastx
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
78 -o '$output'
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
79
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
80 ]]>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
81 </command>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
82 <inputs>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
83 <param format="fasta" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
84 <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
85 <option value="fasta:pro">FASTA protein sequence</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
86 <option value="fasta:nuc">FASTA nucleotide sequence</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
87 <option value="blastout:xml">XML BLAST output</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
88 <option value="blastout:tab">Tabular BLAST output</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
89 <option value="id:uniprot">UniProtKB AC</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
90 <option value="id:ensembl">Ensembl Gene ID</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
91 <option value="id:ncbigene">Entrez Gene ID</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
92 <option value="id:refseqpro">Refseq Protein ID</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
93 </param>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
94
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
95 <conditional name="blast_opts">
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
96 <expand macro="blastdb_selector"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
97 </conditional>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
98
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
99 <expand macro="input_kobasdb"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
100
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
101 <param format="sqlite" name="organismdb" type="data" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
102 <param type="text" argument="--evalue" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
103 <param type="integer" argument="--rank" value="5" min="0" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
104 <param type="integer" argument="--coverage" value="0" min="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
105 <conditional name="ortholog">
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
106 <param name="only" type="select" argument="--ortholog" label="Only use orthologs" help="Whether only use orthologs for cross-species annotation or not, default NO (if only use orthologs, please provide the species abbreviation of your input)">
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
107 <option value="NO">No</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
108 <option value="YES">Yes</option>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
109 </param>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
110 <when value="YES">
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
111 <expand macro="input_kobasdb"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
112 <conditional name="blast_opts_ortholog">
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
113 <expand macro="blastdb_selector"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
114 </conditional>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
115 </when>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
116 <when value="NO"></when>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
117 </conditional>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
118 </inputs>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
119 <outputs>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
120 <data format="tabular" name="output"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
121 </outputs>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
122
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
123 <tests>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
124 <test>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
125 <param name="infile" value="kobas_annotate_input.fasta"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
126 <param name="intype" value="fasta:pro"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
127 <conditional name="blast_opts">
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
128 <param name="choice" value="fasta"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
129 <param name="fastadb" value="aaa.pep.fasta" />
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
130 </conditional>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
131 <param name="species" value="aaa"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
132 <param name="kobasdb" value="aaa.db"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
133 <param name="organismdb" value="organism.db"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
134 <output name="out_file1" file="kobas_annotate_output.txt"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
135 </test>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
136 </tests>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
137
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
138 <help>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
139 @HELP_KOBAS_INFO@
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
140
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
141 **KOBAS Annotate**
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
142
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
143 Annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations. It allows for both ID mapping and cross-species sequence similarity mapping.
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
144
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
145 @HELP_KOBAS_URL@
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
146 </help>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
147
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
148 <expand macro="kobas_citations"/>
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
149
e3308a2b63f4 planemo upload commit 07ca139d824550801d6f5ba425579a05b884d101
iuc
parents:
diff changeset
150 </tool>