Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_database.xml @ 17:4c9f9d6098eb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
author | dfornika |
---|---|
date | Mon, 06 May 2019 19:42:14 -0400 |
parents | |
children | f005b6efd096 |
comparison
equal
deleted
inserted
replaced
16:d9f190088154 | 17:4c9f9d6098eb |
---|---|
1 <?xml version="1.0"?> | |
2 <tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.8_beta"> | |
3 <macros> | |
4 <xml name="common_params"> | |
5 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> | |
6 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> | |
7 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> | |
8 </xml> | |
9 </macros> | |
10 <description>database builder</description> | |
11 <requirements> | |
12 <requirement type="package" version="2.0.8_beta">kraken2</requirement> | |
13 </requirements> | |
14 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> | |
15 <command detect_errors="exit_code"> | |
16 <![CDATA[ | |
17 python '$__tool_directory__/kraken2_build_database.py' | |
18 '${out_file}' | |
19 --database-type ${database_type.database_type} | |
20 #if $database_type.database_type == "minikraken" | |
21 --minikraken2-version ${database_type.minikraken2_version} | |
22 #else if $database_type.database_type == "standard" | |
23 --threads \${GALAXY_SLOTS:-1} | |
24 --kmer-len ${database_type.kmer_len} | |
25 --minimizer-len ${database_type.minimizer_len} | |
26 --minimizer-spaces ${database_type.minimizer_spaces} | |
27 #else if $database_type.database_type == "special" | |
28 --threads \${GALAXY_SLOTS:-1} | |
29 --special-database-type ${database_type.special_database_type} | |
30 --kmer-len ${database_type.kmer_len} | |
31 --minimizer-len ${database_type.minimizer_len} | |
32 --minimizer-spaces ${database_type.minimizer_spaces} | |
33 #else if $database_type.database_type == "custom" | |
34 --threads \${GALAXY_SLOTS:-1} | |
35 --custom-fasta ${database_type.custom_fasta} | |
36 --custom-database-name ${database_type.custom_database_name} | |
37 --kmer-len ${database_type.kmer_len} | |
38 --minimizer-len ${database_type.minimizer_len} | |
39 --minimizer-spaces ${database_type.minimizer_spaces} | |
40 #end if | |
41 ]]> | |
42 </command> | |
43 <inputs> | |
44 <conditional name="database_type"> | |
45 <param name="database_type" type="select" multiple="false" label="Database Type"> | |
46 <option value="standard">Standard</option> | |
47 <option value="minikraken">MiniKraken</option> | |
48 <option value="special">Special</option> | |
49 <option value="custom">Custom</option> | |
50 </param> | |
51 <when value="standard"> | |
52 <expand macro="common_params" /> | |
53 </when> | |
54 <when value="minikraken"> | |
55 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> | |
56 <option value="v2">Version 2</option> | |
57 <option value="v1">Version 1</option> | |
58 </param> | |
59 </when> | |
60 <when value="special"> | |
61 <param name="special_database_type" type="select" multiple="false" label="Select database to build"> | |
62 <option value="greengenes">Greengenes</option> | |
63 <option value="silva">Silva</option> | |
64 <option value="rdp">RDP</option> | |
65 </param> | |
66 <expand macro="common_params" /> | |
67 </when> | |
68 <when value="custom"> | |
69 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> | |
70 <param name="custom_database_name" type="text" label="Name for this database" /> | |
71 <expand macro="common_params" /> | |
72 </when> | |
73 | |
74 </conditional> | |
75 </inputs> | |
76 <outputs> | |
77 <data name="out_file" format="data_manager_json" /> | |
78 </outputs> | |
79 <help> | |
80 </help> | |
81 <citations> | |
82 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> | |
83 </citations> | |
84 </tool> |