Mercurial > repos > dfornika > data_manager_build_bracken_database
diff data_manager/bracken_build_database.xml @ 0:911bb6c95bf8 draft default tip
"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit d0b060e7d9cc9fd89926dbc07fc93c8a1471b3fe-dirty"
author | dfornika |
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date | Thu, 24 Oct 2019 17:44:45 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/bracken_build_database.xml Thu Oct 24 17:44:45 2019 -0400 @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5_galaxy0" profile="19.01"> + <description>bracken database builder</description> + <requirements> + <requirement type="package" version="2.5">bracken</requirement> + <requirement type="package" version="2.0.8_beta">kraken2</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/bracken_build_database.py' + '${out_file}' + --kraken-db '${kraken_db.fields.path}' + --threads \${GALAXY_SLOTS:-1} + --kmer-len ${kmer_len} + --read-len ${read_len} + --database-name '${database_name}' + ]]> + </command> + <inputs> + <param name="kraken_db" type="select"> + <options from_data_table="kraken2_databases"> + <validator type="no_options" message="No Kraken2 databases are available" /> + </options> + </param> + <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" /> + <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" /> + <param name="database_name" type="text" label="Database Name" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <test> + <param name="kraken_db" value="test_entry" /> + <param name="database_name" value="database" /> + <output name="out_file"> + <assert_contents> + <has_text text="test_db/database100mers.kmer_distrib" /> + </assert_contents> + </output> + </test> + </tests> + <help> + </help> + <citations> + <citation type="doi">10.7717/peerj-cs.104</citation> + </citations> +</tool>