Mercurial > repos > iuc > data_manager_build_bracken_database

comparison data_manager/bracken_build_database.xml @ 0:0891b7492a3c 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 74e81c69c8806d98beb15a889741bcd702866ce3"
author iuc
date Sun, 20 Oct 2019 09:36:55 -0400
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children b980e034a6df
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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>