Mercurial > repos > dfornika > data_manager_build_kraken2_database

view data_manager/kraken2_build_minikraken.xml @ 12:039a65ff445d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author dfornika
date Tue, 05 Mar 2019 15:11:05 -0500
parents 1dc93ae264e6
children 512c57d5d277
line wrap: on
line source

<?xml version="1.0"?>
<tool id="kraken2_build_minikraken" name="Kraken2 MiniKraken2 Database Builder" tool_type="manage_data" version="2.0.7_beta">
    <description>database builder</description>
    <requirements>
        <requirement type="package" version="2.0.7_beta">kraken2</requirement>
    </requirements>
    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
    <command detect_errors="exit_code">
    <![CDATA[
        python '$__tool_directory__/kraken2_build_minikraken.py'
          '${out_file}'
          --threads \${GALAXY_SLOTS:-1}
	  --minikraken2-version ${minikraken2_version}
    ]]>
    </command>
    <inputs>
        <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
            <option value="v1">Version 1</option>
	    <option value="v2">Version 2</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>
    </help>
    <citations>
        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
    </citations>
</tool>