Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_special.xml @ 7:ae6180bdb1e9 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author | dfornika |
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date | Mon, 04 Mar 2019 19:20:33 -0500 |
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6:ce101123d015 | 7:ae6180bdb1e9 |
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1 <?xml version="1.0"?> | |
2 <tool id="kraken2_build_special" name="Kraken2 Special Database Builder" tool_type="manage_data" version="2.0.7_beta"> | |
3 <description>database builder</description> | |
4 <requirements> | |
5 <requirement type="package" version="2.0.7_beta">kraken2</requirement> | |
6 </requirements> | |
7 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> | |
8 <command detect_errors="exit_code"> | |
9 <![CDATA[ | |
10 python '$__tool_directory__/kraken2_build_special.py' | |
11 '${out_file}' | |
12 --db-type ${db_type} | |
13 --threads \${GALAXY_SLOTS:-1} | |
14 --kmer-len ${kmer_len} | |
15 --minimizer-len ${minimizer_len} | |
16 --minimizer-spaces ${minimizer_spaces} | |
17 ]]> | |
18 </command> | |
19 <inputs> | |
20 <param name="db_type" type="select" multiple="false" label="Select database to build"> | |
21 <option value="greengenes">Greengenes</option> | |
22 <option value="silva">Silva</option> | |
23 <option value="rdp">RDP</option> | |
24 </param> | |
25 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> | |
26 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> | |
27 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> | |
28 </inputs> | |
29 <outputs> | |
30 <data name="out_file" format="data_manager_json" /> | |
31 </outputs> | |
32 <help> | |
33 </help> | |
34 <citations> | |
35 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> | |
36 </citations> | |
37 </tool> |