Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_standard.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 |
parents | |
children | ce101123d015 |
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-1:000000000000 | 0:7e43f66abe9d |
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1 <?xml version="1.0"?> | |
2 <tool id="kraken2_build_standard" name="Kraken2 Standard Database Builder (subprocess)" 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_standard.py' | |
11 '${out_file}' | |
12 --threads \${GALAXY_SLOTS:-1} | |
13 --kmer-len ${kmer_len} | |
14 --minimizer-len ${minimizer_len} | |
15 --minimizer-spaces ${minimizer_spaces} | |
16 ]]> | |
17 </command> | |
18 <inputs> | |
19 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> | |
20 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> | |
21 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> | |
22 </inputs> | |
23 <outputs> | |
24 <data name="out_file" format="data_manager_json" /> | |
25 </outputs> | |
26 <help> | |
27 </help> | |
28 <citations> | |
29 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> | |
30 </citations> | |
31 </tool> |