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comparison kobas_annotate.xml @ 4:20f1b45dea63 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kobas commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:50:07 -0500
parents 83b998fa34ea
children
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3:83b998fa34ea 4:20f1b45dea63
1 <tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@"> 1 <tool id="kobas_annotate" name="KOBAS Annotate" version="@TOOL_VERSION@">
2 <description>KEGG Orthology Based Annotation System</description> 2 <description>KEGG Orthology Based Annotation System</description>
3 <macros> 3 <macros>
4 <import>kobas_macros.xml</import> 4 <import>kobas_macros.xml</import>
5 </macros> 5 </macros>
6 6
8 8
9 <stdio> 9 <stdio>
10 <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/> 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."/> 11 <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>
12 </stdio> 12 </stdio>
13 <command> 13 <command><![CDATA[
14 <![CDATA[ 14 ## create the KOBAS directories
15 mkdir sqlite &&
16 mkdir seq_pep &&
15 17
16 ## create the KOBAS directories 18 #if $blast_opts.choice == 'local':
17 mkdir sqlite && 19 #set $blast_path = $blast_opts.localdb.fields.path
18 mkdir seq_pep && 20 #elif $blast_opts.choice == 'fasta':
21 makeblastdb
22 -in '$blast_opts.fastadb'
23 -dbtype 'prot'
24 -out 'seq_pep/${species}.pep.fasta' &&
25 #else:
26 #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,'blastdb')
27 #end if
19 28
20 #if $blast_opts.choice == 'local': 29 ## create the database symlinks to comply with how KOBAS wants them
21 #set $blast_path = $blast_opts.localdb.fields.path 30 ln -s '$organismdb' sqlite/organism.db &&
22 #else if $blast_opts.choice == 'fasta': 31 ln -s '$kobasdb' 'sqlite/${species}.db' &&
23 makeblastdb
24 -in '$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 32
31 ## create the database symlinks to comply with how KOBAS wants them 33 #if $blast_opts.choice != 'fasta':
32 ln -s '$organismdb' sqlite/organism.db && 34 ln -s '${blast_path}.phr' 'seq_pep/${species}.pep.fasta.phr' &&
33 ln -s '$kobasdb' 'sqlite/${species}.db' && 35 ln -s '${blast_path}.pin' 'seq_pep/${species}.pep.fasta.pin' &&
36 ln -s '${blast_path}.psq' 'seq_pep/${species}.pep.fasta.psq' && ls -l seq_pep/ &&
37 #end if
34 38
35 #if $blast_opts.choice != 'fasta': 39 ## create the orthologe database symlinks to comply with how KOBAS wants them
36 ln -s '${blast_path}.phr' 'seq_pep/${species}.pep.fasta.phr' && 40 #if $ortholog.only == 'YES' and str($ortholog.species) != str($species):
37 ln -s '${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
41 ## create the orthologe database symlinks to comply with how KOBAS wants them 42 #if $ortholog.blast_opts_ortholog.choice == 'local':
42 #if $ortholog.only == 'YES' and str($ortholog.species) != str($species): 43 #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path
44 #elif $ortholog.blast_opts_ortholog.choice == 'fasta':
45 makeblastdb
46 -in '$ortholog.blast_opts_ortholog.fastadb'
47 -dbtype 'prot'
48 -out 'seq_pep/${ortholog.species}.pep.fasta' &&
49 #else:
50 #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,'blastdb')
51 #end if
43 52
44 #if $ortholog.blast_opts_ortholog.choice == 'local': 53 ln -s '$ortholog.kobasdb' 'sqlite/${ortholog.species}.db' &&
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 54
55 ln -s '$ortholog.kobasdb' 'sqlite/${ortholog.species}.db' && 55 #if $blast_opts.choice != 'fasta':
56 ln -s '${blast_path}.phr' 'seq_pep/${ortholog.species}.pep.fasta.phr' &&
57 ln -s '${blast_path}.pin' 'seq_pep/${ortholog.species}.pep.fasta.pin' &&
58 ln -s '${blast_path}.psq' 'seq_pep/${ortholog.species}.pep.fasta.psq' &&
59 #end if
60 #end if
56 61
57 #if $blast_opts.choice != 'fasta': 62 kobas-annotate
58 ln -s '${blast_path}.phr' 'seq_pep/${ortholog.species}.pep.fasta.phr' && 63 -i '$infile'
59 ln -s '${blast_path}.pin' 'seq_pep/${ortholog.species}.pep.fasta.pin' && 64 -t '$intype'
60 ln -s '${blast_path}.psq' 'seq_pep/${ortholog.species}.pep.fasta.psq' && 65 -s '$species'
61 #end if 66 -e '$evalue'
62 #end if 67 -r $rank
63 68 -n "\${GALAXY_SLOTS:-4}"
64 kobas-annotate 69 -c $coverage
65 -i '$infile' 70 #if $ortholog.only == 'YES':
66 -t '$intype' 71 -z '$ortholog.species'
67 -s '$species' 72 #end if
68 -e '$evalue' 73 -y seq_pep
69 -r $rank 74 -q sqlite
70 -n "\${GALAXY_SLOTS:-4}" 75 -p blastp
71 -c $coverage 76 -x blastx
72 #if $ortholog.only == 'YES': 77 -o '$output'
73 -z '$ortholog.species' 78 ]]></command>
74 #end if
75 -y seq_pep
76 -q sqlite
77 -p blastp
78 -x blastx
79 -o '$output'
80
81 ]]>
82 </command>
83 <inputs> 79 <inputs>
84 <param format="fasta,tabular,txt" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/> 80 <param argument="--infile" type="data" format="fasta,tabular,txt" label="Input file" help="Input data file matching the input type."/>
85 <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro"> 81 <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">
86 <option value="fasta:pro">FASTA protein sequence</option> 82 <option value="fasta:pro">FASTA protein sequence</option>
87 <option value="fasta:nuc">FASTA nucleotide sequence</option> 83 <option value="fasta:nuc">FASTA nucleotide sequence</option>
88 <option value="blastout:xml">XML BLAST output</option> 84 <option value="blastout:xml">XML BLAST output</option>
89 <option value="blastout:tab">Tabular BLAST output</option> 85 <option value="blastout:tab">Tabular BLAST output</option>
97 <expand macro="blastdb_selector"/> 93 <expand macro="blastdb_selector"/>
98 </conditional> 94 </conditional>
99 95
100 <expand macro="input_kobasdb"/> 96 <expand macro="input_kobasdb"/>
101 97
102 <param format="sqlite" name="organismdb" type="data" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/> 98 <param name="organismdb" type="data" format="sqlite" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/>
103 <param type="text" argument="--evalue" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/> 99 <param argument="--evalue" type="text" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>
104 <param type="integer" argument="--rank" value="5" min="0" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/> 100 <param argument="--rank" type="integer" min="0" value="5" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>
105 <param type="integer" argument="--coverage" value="0" min="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/> 101 <param argument="--coverage" type="integer" min="0" value="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>
106 <conditional name="ortholog"> 102 <conditional name="ortholog">
107 <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)"> 103 <param name="only" argument="--ortholog" type="select" 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)">
108 <option value="NO">No</option> 104 <option value="NO">No</option>
109 <option value="YES">Yes</option> 105 <option value="YES">Yes</option>
110 </param> 106 </param>
111 <when value="YES"> 107 <when value="YES">
112 <expand macro="input_kobasdb"/> 108 <expand macro="input_kobasdb"/>
116 </when> 112 </when>
117 <when value="NO"></when> 113 <when value="NO"></when>
118 </conditional> 114 </conditional>
119 </inputs> 115 </inputs>
120 <outputs> 116 <outputs>
121 <data format="tabular" name="output"/> 117 <data name="output" format="tabular"/>
122 </outputs> 118 </outputs>
123 119
124 <tests> 120 <tests>
125 <test> 121 <test>
126 <param name="infile" value="kobas_annotate_input.fasta"/> 122 <param name="infile" value="kobas_annotate_input.fasta"/>
130 <param name="fastadb" value="aaa.pep.fasta" /> 126 <param name="fastadb" value="aaa.pep.fasta" />
131 </conditional> 127 </conditional>
132 <param name="species" value="aaa"/> 128 <param name="species" value="aaa"/>
133 <param name="kobasdb" value="aaa.db"/> 129 <param name="kobasdb" value="aaa.db"/>
134 <param name="organismdb" value="organism.db"/> 130 <param name="organismdb" value="organism.db"/>
135 <output name="out_file1" file="kobas_annotate_output.txt"/> 131 <output name="output" file="kobas_annotate_output.txt"/>
136 </test> 132 </test>
137 </tests> 133 </tests>
138 134
139 <help> 135 <help>
140 @HELP_KOBAS_INFO@ 136 @HELP_KOBAS_INFO@