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comparison data_manager/kraken2_build_database.xml @ 0:a7c8b9cd05da draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
author iuc
date Thu, 30 May 2019 03:02:57 -0400
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children 5348b6e2823d
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-1:000000000000 0:a7c8b9cd05da
1 <?xml version="1.0"?>
2 <tool id="kraken2_build_database" name="Kraken2" 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 ${database_type.skip_maps}
36 --custom-fasta ${database_type.custom_fasta}
37 --custom-database-name ${database_type.custom_database_name}
38 --kmer-len ${database_type.kmer_len}
39 --minimizer-len ${database_type.minimizer_len}
40 --minimizer-spaces ${database_type.minimizer_spaces}
41 #end if
42 ]]>
43 </command>
44 <inputs>
45 <conditional name="database_type">
46 <param name="database_type" type="select" multiple="false" label="Database Type">
47 <option value="standard">Standard</option>
48 <option value="minikraken">MiniKraken</option>
49 <option value="special">Special</option>
50 <option value="custom">Custom</option>
51 </param>
52 <when value="standard">
53 <expand macro="common_params" />
54 </when>
55 <when value="minikraken">
56 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
57 <option value="v2">Version 2</option>
58 <option value="v1">Version 1</option>
59 </param>
60 </when>
61 <when value="special">
62 <param name="special_database_type" type="select" multiple="false" label="Select database to build">
63 <option value="greengenes">Greengenes</option>
64 <option value="silva">Silva</option>
65 <option value="rdp">RDP</option>
66 </param>
67 <expand macro="common_params" />
68 </when>
69 <when value="custom">
70 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
71 <param name="custom_database_name" type="text" label="Name for this database" />
72 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
73 <expand macro="common_params" />
74 </when>
75
76 </conditional>
77 </inputs>
78 <outputs>
79 <data name="out_file" format="data_manager_json" />
80 </outputs>
81 <tests>
82 <test>
83 <param name="database_type" value="custom" />
84 <param name="custom_fasta" value="adapter.fa" />
85 <param name="custom_database_name" value="database" />
86 <param name="skip_maps" value="true" />
87 <output name="out_file" value="kraken2_custom_data_manager.json" />
88 </test>
89 </tests>
90 <help>
91 </help>
92 <citations>
93 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
94 </citations>
95 </tool>