Mercurial > repos > iuc > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_database.xml @ 5:0d6cdde238ba 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 648fe4911ce49173697f314d70e63e0de95b7e66"
author iuc
date Mon, 08 Nov 2021 15:40:07 +0000
parents 5f4b0a3cb38b
children 691a1055a112
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4:5f4b0a3cb38b 5:0d6cdde238ba
21 python '$__tool_directory__/kraken2_build_database.py' 21 python '$__tool_directory__/kraken2_build_database.py'
22 '${out_file}' 22 '${out_file}'
23 --database-type ${database_type.database_type} 23 --database-type ${database_type.database_type}
24 #if $database_type.database_type == "minikraken" 24 #if $database_type.database_type == "minikraken"
25 --minikraken2-version ${database_type.minikraken2_version} 25 --minikraken2-version ${database_type.minikraken2_version}
26 #else if $database_type.database_type == "standard" 26 #else if $database_type.database_type == "standard_prebuilt"
27 --standard-prebuilt-size ${database_type.standard_prebuilt_size}
28 #if $database_type.prebuilt_date_custom != ""
29 --prebuilt-date ${database_type.prebuilt_date_custom}
30 #else
31 --prebuilt-date ${database_type.prebuilt_date}
32 #end if
33 #else if $database_type.database_type == "standard_local_build"
27 --threads \${GALAXY_SLOTS:-1} 34 --threads \${GALAXY_SLOTS:-1}
28 --kmer-len ${database_type.kmer_len} 35 --kmer-len ${database_type.kmer_len}
29 --minimizer-len ${database_type.minimizer_len} 36 --minimizer-len ${database_type.minimizer_len}
30 --minimizer-spaces ${database_type.minimizer_spaces} 37 --minimizer-spaces ${database_type.minimizer_spaces}
31 --load-factor ${database_type.load_factor} 38 --load-factor ${database_type.load_factor}
52 ]]> 59 ]]>
53 </command> 60 </command>
54 <inputs> 61 <inputs>
55 <conditional name="database_type"> 62 <conditional name="database_type">
56 <param name="database_type" type="select" multiple="false" label="Database Type"> 63 <param name="database_type" type="select" multiple="false" label="Database Type">
57 <option value="standard">Standard</option> 64 <option value="standard_local_build">Standard, Local Build</option>
65 <option value="standard_prebuilt">Standard, Pre-Built</option>
58 <option value="minikraken">MiniKraken</option> 66 <option value="minikraken">MiniKraken</option>
59 <option value="special">Special</option> 67 <option value="special">Special</option>
60 <option value="custom">Custom</option> 68 <option value="custom">Custom</option>
61 </param> 69 </param>
62 <when value="standard"> 70 <when value="standard_local_build">
63 <expand macro="common_params" /> 71 <expand macro="common_params" />
72 </when>
73 <when value="standard_prebuilt">
74 <param name="standard_prebuilt_size" type="select" multiple="false" label="Select size of prebuilt database to download">
75 <option value="full">Standard-Full (~50 GB)</option>
76 <option value="16">Standard-16 (~16 GB)</option>
77 <option value="8">Standard-8 (~8 GB)</option>
78 </param>
79 <param name="prebuilt_date" type="select" multiple="false" optional="true" label="Select database build date">
80 <option value="2021-05-17">May 17, 2021</option>
81 <option value="2020-12-02">December 2, 2020</option>
82 </param>
83 <param name="prebuilt_date_custom" type="text" label="Custom date (YYYY-MM-DD)" help="Any text here will overwrite the selected date above." />
64 </when> 84 </when>
65 <when value="minikraken"> 85 <when value="minikraken">
66 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> 86 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
67 <option value="v2">Version 2</option> 87 <option value="v2">Version 2</option>
68 <option value="v1">Version 1</option> 88 <option value="v1">Version 1</option>