Mercurial > repos > iuc > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_database.xml @ 1:5348b6e2823d 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 5f6f447482ad7e127af78204ffd583c51509a0be
author iuc
date Sat, 03 Aug 2019 05:30:50 -0400
parents a7c8b9cd05da
children d861448f78b9
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0:a7c8b9cd05da 1:5348b6e2823d
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta"> 2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta+galaxy1">
3 <macros> 3 <macros>
4 <xml name="common_params"> 4 <xml name="common_params">
5 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> 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" /> 6 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
7 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> 7 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
8 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
8 </xml> 9 </xml>
9 </macros> 10 </macros>
10 <description>database builder</description> 11 <description>database builder</description>
11 <requirements> 12 <requirements>
12 <requirement type="package" version="2.0.8_beta">kraken2</requirement> 13 <requirement type="package" version="2.0.8_beta">kraken2</requirement>
22 #else if $database_type.database_type == "standard" 23 #else if $database_type.database_type == "standard"
23 --threads \${GALAXY_SLOTS:-1} 24 --threads \${GALAXY_SLOTS:-1}
24 --kmer-len ${database_type.kmer_len} 25 --kmer-len ${database_type.kmer_len}
25 --minimizer-len ${database_type.minimizer_len} 26 --minimizer-len ${database_type.minimizer_len}
26 --minimizer-spaces ${database_type.minimizer_spaces} 27 --minimizer-spaces ${database_type.minimizer_spaces}
28 ${database_type.clean}
27 #else if $database_type.database_type == "special" 29 #else if $database_type.database_type == "special"
28 --threads \${GALAXY_SLOTS:-1} 30 --threads \${GALAXY_SLOTS:-1}
29 --special-database-type ${database_type.special_database_type} 31 --special-database-type ${database_type.special_database_type}
30 --kmer-len ${database_type.kmer_len} 32 --kmer-len ${database_type.kmer_len}
31 --minimizer-len ${database_type.minimizer_len} 33 --minimizer-len ${database_type.minimizer_len}
32 --minimizer-spaces ${database_type.minimizer_spaces} 34 --minimizer-spaces ${database_type.minimizer_spaces}
35 ${database_type.clean}
33 #else if $database_type.database_type == "custom" 36 #else if $database_type.database_type == "custom"
34 --threads \${GALAXY_SLOTS:-1} 37 --threads \${GALAXY_SLOTS:-1}
35 ${database_type.skip_maps} 38 ${database_type.skip_maps}
36 --custom-fasta ${database_type.custom_fasta} 39 --custom-fasta ${database_type.custom_fasta}
37 --custom-database-name ${database_type.custom_database_name} 40 --custom-database-name ${database_type.custom_database_name}
38 --kmer-len ${database_type.kmer_len} 41 --kmer-len ${database_type.kmer_len}
39 --minimizer-len ${database_type.minimizer_len} 42 --minimizer-len ${database_type.minimizer_len}
40 --minimizer-spaces ${database_type.minimizer_spaces} 43 --minimizer-spaces ${database_type.minimizer_spaces}
44 ${database_type.clean}
41 #end if 45 #end if
42 ]]> 46 ]]>
43 </command> 47 </command>
44 <inputs> 48 <inputs>
45 <conditional name="database_type"> 49 <conditional name="database_type">
52 <when value="standard"> 56 <when value="standard">
53 <expand macro="common_params" /> 57 <expand macro="common_params" />
54 </when> 58 </when>
55 <when value="minikraken"> 59 <when value="minikraken">
56 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> 60 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
57 <option value="v2">Version 2</option> 61 <option value="v2">Version 2</option>
58 <option value="v1">Version 1</option> 62 <option value="v1">Version 1</option>
59 </param> 63 </param>
60 </when> 64 </when>
61 <when value="special"> 65 <when value="special">
62 <param name="special_database_type" type="select" multiple="false" label="Select database to build"> 66 <param name="special_database_type" type="select" multiple="false" label="Select database to build">
70 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> 74 <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" /> 75 <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." /> 76 <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" /> 77 <expand macro="common_params" />
74 </when> 78 </when>
75
76 </conditional> 79 </conditional>
77 </inputs> 80 </inputs>
78 <outputs> 81 <outputs>
79 <data name="out_file" format="data_manager_json" /> 82 <data name="out_file" format="data_manager_json" />
80 </outputs> 83 </outputs>