Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_custom.xml @ 2:cf0cda80b659 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
author | dfornika |
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date | Thu, 28 Feb 2019 18:18:01 -0500 |
parents | |
children | 988c436ad798 |
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1:32d04371ed19 | 2:cf0cda80b659 |
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1 <?xml version="1.0"?> | |
2 <tool id="kraken2_build_custom" name="Kraken2 Custom 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 --fasta ${input_fasta} | |
14 --kmer-len ${kmer_len} | |
15 --minimizer-len ${minimizer_len} | |
16 --minimizer-spaces ${minimizer_spaces} | |
17 ]]> | |
18 </command> | |
19 <inputs> | |
20 <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> | |
21 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> | |
22 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> | |
23 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> | |
24 </inputs> | |
25 <outputs> | |
26 <data name="out_file" format="data_manager_json" /> | |
27 </outputs> | |
28 <help> | |
29 </help> | |
30 <citations> | |
31 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> | |
32 </citations> | |
33 </tool> |