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comparison kobas_annotate.xml @ 0:720b1beabad6 draft

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planemo upload commit 5dd86ae785ae71f697aab8ede735f394b39ad7bc-dirty
author iuc
date Sat, 05 Nov 2016 09:20:51 -0400
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1 <tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@">
2 <description>KEGG Orthology Based Annotation System</description>
3 <macros>
4 <import>kobas_macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/>
11 <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>
12 </stdio>
13 <command>
14 <![CDATA[
15
16 ## create the KOBAS directories
17 mkdir sqlite &&
18 mkdir seq_pep &&
19
20 #if $blast_opts.choice == 'local':
21 #set $blast_path = $blast_opts.localdb.fields.path
22 #else if $blast_opts.choice == 'fasta':
23 makeblastdb
24 -in '$blast_opts.fastadb'
25 -dbtype 'prot'
26 -out 'seq_pep/${species}.pep.fasta' &&
27 #else:
28 #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,'blastdb')
29 #end if
30
31 ## create the database symlinks to comply with how KOBAS wants them
32 ln -s '$organismdb' sqlite/organism.db &&
33 ln -s '$kobasdb' 'sqlite/${species}.db' &&
34
35 #if $blast_opts.choice != 'fasta':
36 ln -s '${blast_path}.phr' 'seq_pep/${species}.pep.fasta.phr' &&
37 ln -s '${blast_path}.pin' 'seq_pep/${species}.pep.fasta.pin' &&
38 ln -s '${blast_path}.psq' 'seq_pep/${species}.pep.fasta.psq' && ls -l seq_pep/ &&
39 #end if
40
41 ## create the orthologe database symlinks to comply with how KOBAS wants them
42 #if $ortholog.only == 'YES' and str($ortholog.species) != str($species):
43
44 #if $ortholog.blast_opts_ortholog.choice == 'local':
45 #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path
46 #else if $ortholog.blast_opts_ortholog.choice == 'fasta':
47 makeblastdb
48 -in '$ortholog.blast_opts_ortholog.fastadb'
49 -dbtype 'prot'
50 -out 'seq_pep/${ortholog.species}.pep.fasta' &&
51 #else:
52 #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,'blastdb')
53 #end if
54
55 ln -s '$ortholog.kobasdb' 'sqlite/${ortholog.species}.db' &&
56
57 #if $blast_opts.choice != 'fasta':
58 ln -s '${blast_path}.phr' 'seq_pep/${ortholog.species}.pep.fasta.phr' &&
59 ln -s '${blast_path}.pin' 'seq_pep/${ortholog.species}.pep.fasta.pin' &&
60 ln -s '${blast_path}.psq' 'seq_pep/${ortholog.species}.pep.fasta.psq' &&
61 #end if
62 #end if
63
64 kobas-annotate
65 -i '$infile'
66 -t '$intype'
67 -s '$species'
68 -e '$evalue'
69 -r $rank
70 -c $coverage
71 #if $ortholog.only == 'YES':
72 -z '$ortholog.species'
73 #end if
74 -y seq_pep
75 -q sqlite
76 -p blastp
77 -x blastx
78 -o '$output'
79
80 ]]>
81 </command>
82 <inputs>
83 <param format="fasta" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>
84 <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">
85 <option value="fasta:pro">FASTA protein sequence</option>
86 <option value="fasta:nuc">FASTA nucleotide sequence</option>
87 <option value="blastout:xml">XML BLAST output</option>
88 <option value="blastout:tab">Tabular BLAST output</option>
89 <option value="id:uniprot">UniProtKB AC</option>
90 <option value="id:ensembl">Ensembl Gene ID</option>
91 <option value="id:ncbigene">Entrez Gene ID</option>
92 <option value="id:refseqpro">Refseq Protein ID</option>
93 </param>
94
95 <conditional name="blast_opts">
96 <expand macro="blastdb_selector"/>
97 </conditional>
98
99 <expand macro="input_kobasdb"/>
100
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"/>
102 <param type="text" argument="--evalue" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>
103 <param type="integer" argument="--rank" value="5" min="0" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>
104 <param type="integer" argument="--coverage" value="0" min="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>
105 <conditional name="ortholog">
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)">
107 <option value="NO">No</option>
108 <option value="YES">Yes</option>
109 </param>
110 <when value="YES">
111 <expand macro="input_kobasdb"/>
112 <conditional name="blast_opts_ortholog">
113 <expand macro="blastdb_selector"/>
114 </conditional>
115 </when>
116 <when value="NO"></when>
117 </conditional>
118 </inputs>
119 <outputs>
120 <data format="tabular" name="output"/>
121 </outputs>
122
123 <tests>
124 <test>
125 <param name="infile" value="kobas_annotate_input.fasta"/>
126 <param name="intype" value="fasta:pro"/>
127 <conditional name="blast_opts">
128 <param name="choice" value="fasta"/>
129 <param name="fastadb" value="aaa.pep.fasta" />
130 </conditional>
131 <param name="species" value="aaa"/>
132 <param name="kobasdb" value="aaa.db"/>
133 <param name="organismdb" value="organism.db"/>
134 <output name="out_file1" file="kobas_annotate_output.txt"/>
135 </test>
136 </tests>
137
138 <help>
139 @HELP_KOBAS_INFO@
140
141 **KOBAS Annotate**
142
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.
144
145 @HELP_KOBAS_URL@
146 </help>
147
148 <expand macro="kobas_citations"/>
149
150 </tool>