Mercurial > repos > greg > data_manager_pima_pv_downloader

view data_manager/pima_pv_downloader.xml @ 0:9972e1e07347 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Mon, 12 Dec 2022 15:02:14 +0000
parents
children
line wrap: on
line source

<tool id="pima_pv_downloader" name="PIMA pv data manager" tool_type="manage_data" profile="21.09" version="1.0.0">
    <description>Download plasmids_and_vectors.fasta files</description>
    <requirements>
        <requirement type="package" version="3.10.6">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/pima_pv_downloader.py'
--out_file '$out_file'
--url '$url'
    ]]>
    </command>
    <inputs>
        <param name="url" type="text" value="http://pima.appliedbinf.com/data/plasmids_and_vectors.fasta" label="URL to download the plasmids_and_vectors.fasta file"/>
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="url" value="http://pima.appliedbinf.com/data/plasmids_and_vectors.fasta"/>
            <output name="out_file" value="pima_pv.json" compare="contains"/>
        </test>
    </tests>
    <help><![CDATA[
This tool downloads the current PIMA plasmids_and_vectors.fasta file for use by various PIMA tools.
    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41598-019-49700-1</citation>
    </citations>
</tool>