Mercurial > repos > iuc > data_manager_build_bracken_database

comparison data_manager/bracken_build_database.xml @ 1:9059edc96a85 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
author iuc
date Sun, 19 Jan 2020 04:33:53 -0500
parents c2e4127fb5bf
children 3c7d2c84cb09
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0:c2e4127fb5bf 1:9059edc96a85
5 <requirement type="package" version="2.5">bracken</requirement> 5 <requirement type="package" version="2.5">bracken</requirement>
6 <requirement type="package" version="2.0.8_beta">kraken2</requirement> 6 <requirement type="package" version="2.0.8_beta">kraken2</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #import os
11 #set db_dir = os.path.basename($kraken_db.fields.path)
12
13 mkdir '$db_dir' &&
14 ln -s '${kraken_db.fields.path}'/* '$db_dir/' &&
10 python '$__tool_directory__/bracken_build_database.py' 15 python '$__tool_directory__/bracken_build_database.py'
11 '${out_file}' 16 '${out_file}'
12 --kraken-db '${kraken_db.fields.path}' 17 --kraken-db '$db_dir'
13 --threads \${GALAXY_SLOTS:-1} 18 --threads \${GALAXY_SLOTS:-1}
14 --kmer-len ${kmer_len} 19 --kmer-len ${kmer_len}
15 --read-len ${read_len} 20 --read-len ${read_len}
16 --database-name '${database_name}' 21 --database-name '${database_name}'
17 ]]> 22 ]]>