Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_standard_database_builder.xml @ 0:7e43f66abe9d draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit cc42cd530378bfa3df83b08b6b41aaf2f5072b49-dirty
author | dfornika |
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date | Thu, 28 Feb 2019 02:32:38 -0500 |
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1 <?xml version="1.0"?> | |
2 <tool id="kraken2_standard_database_builder" name="Kraken2 Standard 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 $NF}'</version_command> | |
8 <command detect_errors="exit_code"> | |
9 <![CDATA[ | |
10 #import datetime | |
11 #set kraken2_db_name = datetime.date.today().strftime('%Y-%m-%d') + "_standard" | |
12 mkdir kraken2-database && cd kraken2-database && | |
13 kraken2-build | |
14 --standard | |
15 --threads \${GALAXY_SLOTS:-1} | |
16 --db '${kraken2_db_name}' | |
17 --kmer-len ${kmer_len} | |
18 --minimizer-len ${minimizer_len} | |
19 --minimizer-spaces ${minimizer_spaces} && | |
20 cd .. && | |
21 python '$__tool_directory__/make_json.py' --db '${kraken2_db_name}' --out '${out_file}' | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
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> |