Mercurial > repos > dfornika > data_manager_build_bracken_database
comparison 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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1 <?xml version="1.0"?> | |
2 <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5_galaxy0" profile="19.01"> | |
3 <description>bracken database builder</description> | |
4 <requirements> | |
5 <requirement type="package" version="2.5">bracken</requirement> | |
6 <requirement type="package" version="2.0.8_beta">kraken2</requirement> | |
7 </requirements> | |
8 <command> | |
9 <![CDATA[ | |
10 python '$__tool_directory__/bracken_build_database.py' | |
11 '${out_file}' | |
12 --kraken-db '${kraken_db.fields.path}' | |
13 --threads \${GALAXY_SLOTS:-1} | |
14 --kmer-len ${kmer_len} | |
15 --read-len ${read_len} | |
16 --database-name '${database_name}' | |
17 ]]> | |
18 </command> | |
19 <inputs> | |
20 <param name="kraken_db" type="select"> | |
21 <options from_data_table="kraken2_databases"> | |
22 <validator type="no_options" message="No Kraken2 databases are available" /> | |
23 </options> | |
24 </param> | |
25 <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" /> | |
26 <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" /> | |
27 <param name="database_name" type="text" label="Database Name" /> | |
28 </inputs> | |
29 <outputs> | |
30 <data name="out_file" format="data_manager_json" /> | |
31 </outputs> | |
32 <tests> | |
33 <test> | |
34 <param name="kraken_db" value="test_entry" /> | |
35 <param name="database_name" value="database" /> | |
36 <output name="out_file"> | |
37 <assert_contents> | |
38 <has_text text="test_db/database100mers.kmer_distrib" /> | |
39 </assert_contents> | |
40 </output> | |
41 </test> | |
42 </tests> | |
43 <help> | |
44 </help> | |
45 <citations> | |
46 <citation type="doi">10.7717/peerj-cs.104</citation> | |
47 </citations> | |
48 </tool> |