Mercurial > repos > dfornika > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_database.xml @ 18:f005b6efd096 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 a6877055190331683367394d1d1ca6ff47cf4fa7-dirty
author dfornika
date Fri, 24 May 2019 13:39:08 -0400
parents 4c9f9d6098eb
children ffeb852407d6
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17:4c9f9d6098eb 18:f005b6efd096
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kraken2_build_database" name="Kraken2 Database Builder" 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">
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" />
30 --kmer-len ${database_type.kmer_len} 30 --kmer-len ${database_type.kmer_len}
31 --minimizer-len ${database_type.minimizer_len} 31 --minimizer-len ${database_type.minimizer_len}
32 --minimizer-spaces ${database_type.minimizer_spaces} 32 --minimizer-spaces ${database_type.minimizer_spaces}
33 #else if $database_type.database_type == "custom" 33 #else if $database_type.database_type == "custom"
34 --threads \${GALAXY_SLOTS:-1} 34 --threads \${GALAXY_SLOTS:-1}
35 ${database_type.skip_maps}
35 --custom-fasta ${database_type.custom_fasta} 36 --custom-fasta ${database_type.custom_fasta}
36 --custom-database-name ${database_type.custom_database_name} 37 --custom-database-name ${database_type.custom_database_name}
37 --kmer-len ${database_type.kmer_len} 38 --kmer-len ${database_type.kmer_len}
38 --minimizer-len ${database_type.minimizer_len} 39 --minimizer-len ${database_type.minimizer_len}
39 --minimizer-spaces ${database_type.minimizer_spaces} 40 --minimizer-spaces ${database_type.minimizer_spaces}
66 <expand macro="common_params" /> 67 <expand macro="common_params" />
67 </when> 68 </when>
68 <when value="custom"> 69 <when value="custom">
69 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> 70 <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 <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." />
71 <expand macro="common_params" /> 73 <expand macro="common_params" />
72 </when> 74 </when>
73 75
74 </conditional> 76 </conditional>
75 </inputs> 77 </inputs>
76 <outputs> 78 <outputs>
77 <data name="out_file" format="data_manager_json" /> 79 <data name="out_file" format="data_manager_json" />
78 </outputs> 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>
79 <help> 90 <help>
80 </help> 91 </help>
81 <citations> 92 <citations>
82 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> 93 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
83 </citations> 94 </citations>