Mercurial > repos > dave > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_database.xml @ 0:bd47b9f87d67 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
author | dave |
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date | Tue, 01 Dec 2020 16:07:40 +0000 |
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-1:000000000000 | 0:bd47b9f87d67 |
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1 <?xml version="1.0"?> | |
2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0" profile="18.09"> | |
3 <macros> | |
4 <token name="@TOOL_VERSION@">2.1.1</token> | |
5 <xml name="common_params"> | |
6 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> | |
7 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> | |
8 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> | |
9 <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" /> | |
10 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> | |
11 </xml> | |
12 </macros> | |
13 <description>database builder</description> | |
14 <requirements> | |
15 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> | |
16 <requirement type="package" version="3.7">python</requirement> | |
17 </requirements> | |
18 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> | |
19 <command detect_errors="exit_code"> | |
20 <![CDATA[ | |
21 python '$__tool_directory__/kraken2_build_database.py' | |
22 '${out_file}' | |
23 --database-type ${database_type.database_type} | |
24 #if $database_type.database_type == "minikraken" | |
25 --minikraken2-release $database_type.kraken_release | |
26 #if $database_type.kraken_release == "April_2019": | |
27 --minikraken2-version ${database_type.kraken_release.minikraken2_version} | |
28 #end if | |
29 #else if $database_type.database_type == "standard" | |
30 --threads \${GALAXY_SLOTS:-1} | |
31 --kmer-len ${database_type.kmer_len} | |
32 --minimizer-len ${database_type.minimizer_len} | |
33 --minimizer-spaces ${database_type.minimizer_spaces} | |
34 --load-factor ${database_type.load_factor} | |
35 ${database_type.clean} | |
36 #else if $database_type.database_type == "special" | |
37 --threads \${GALAXY_SLOTS:-1} | |
38 --special-database-type ${database_type.special_database_type} | |
39 --kmer-len ${database_type.kmer_len} | |
40 --minimizer-len ${database_type.minimizer_len} | |
41 --minimizer-spaces ${database_type.minimizer_spaces} | |
42 --load-factor ${database_type.load_factor} | |
43 ${database_type.clean} | |
44 #else if $database_type.database_type == "custom" | |
45 --threads \${GALAXY_SLOTS:-1} | |
46 ${database_type.skip_maps} | |
47 --custom-fasta ${database_type.custom_fasta} | |
48 --custom-database-name ${database_type.custom_database_name} | |
49 --kmer-len ${database_type.kmer_len} | |
50 --minimizer-len ${database_type.minimizer_len} | |
51 --minimizer-spaces ${database_type.minimizer_spaces} | |
52 --load-factor ${database_type.load_factor} | |
53 ${database_type.clean} | |
54 #end if | |
55 ]]> | |
56 </command> | |
57 <inputs> | |
58 <conditional name="database_type"> | |
59 <param name="database_type" type="select" multiple="false" label="Database Type"> | |
60 <option value="standard">Standard</option> | |
61 <option value="minikraken">MiniKraken</option> | |
62 <option value="special">Special</option> | |
63 <option value="custom">Custom</option> | |
64 </param> | |
65 <when value="standard"> | |
66 <expand macro="common_params" /> | |
67 </when> | |
68 <when value="minikraken"> | |
69 <conditional name="kraken_release"> | |
70 <param name="minikraken2_release" type="select" multiple="false" label="Select the MiniKraken2 release to download"> | |
71 <option value="April_2019">April 2019</option> | |
72 <option value="March_2020">March 2020</option> | |
73 </param> | |
74 <when value="April_2019"> | |
75 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> | |
76 <option value="v2">Version 2</option> | |
77 <option value="v1">Version 1</option> | |
78 </param> | |
79 </when> | |
80 <when value="March_2020" /> | |
81 </conditional> | |
82 </when> | |
83 <when value="special"> | |
84 <param name="special_database_type" type="select" multiple="false" label="Select database to build"> | |
85 <option value="greengenes">Greengenes</option> | |
86 <option value="silva">Silva</option> | |
87 <option value="rdp">RDP</option> | |
88 </param> | |
89 <expand macro="common_params" /> | |
90 </when> | |
91 <when value="custom"> | |
92 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> | |
93 <param name="custom_database_name" type="text" label="Name for this database" /> | |
94 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> | |
95 <expand macro="common_params" /> | |
96 </when> | |
97 </conditional> | |
98 </inputs> | |
99 <outputs> | |
100 <data name="out_file" format="data_manager_json" /> | |
101 </outputs> | |
102 <tests> | |
103 <test> | |
104 <param name="database_type" value="custom" /> | |
105 <param name="custom_fasta" value="adapter.fa" /> | |
106 <param name="custom_database_name" value="database" /> | |
107 <param name="skip_maps" value="true" /> | |
108 <output name="out_file" value="kraken2_custom_data_manager.json" /> | |
109 </test> | |
110 </tests> | |
111 <help> | |
112 </help> | |
113 <citations> | |
114 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> | |
115 </citations> | |
116 </tool> |