Mercurial > repos > estrain > amrfinderplus_db

view data_manager_amrfinderplus/data_manager/data_manager_amrfinderplus.xml @ 0:5ba68abd41f6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Tue, 24 May 2022 11:46:19 +0000
parents
children
line wrap: on
line source

<tool id="data_manager_amrfinderplus" name="AMRFinderPlus Data Manger" tool_type="manage_data" version="0.0.3" profile="20.01">
    <requirements>
        <requirement type="package">blast</requirement>
        <requirement type="package">hmmer</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/data_manager_amrfinderplus.py --name $amrdbname --out ${output_file};
    ]]></command>
    <inputs>
      <param name="amrdbname" type="text" value="latest" label="Release Version - Note: only latest release is supported"/>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help>
    </help>
    <citations>
     Refer to https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/ for latest database version number.
    </citations>
</tool>