view data_manager/data_manager_plant_tribes_scaffolds_download.xml @ 4:93253aebaf2e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"

<tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.1.1" tool_type="manage_data">
    <description></description>
    <requirements>
        <requirement type="package" version="3.8.3">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py
--name '$name'
--description '$description'
--web_url '$web_url'
--config_web_url '$config_web_url'
--out_file '$out_file']]>
    </command>
    <inputs>
        <param name="name" type="text" value="" label="Data table entry unique ID"/>
        <param name="description" type="text" value="" label="Description of the data" help="Value is optional"/>
        <param name="web_url" type="text" value="" label="URL for downloading scaffolds" help="Must be same version as configs" optional="False" />
        <param name="config_web_url" type="text" value="" label="URL for downloading configs" help="Must be same version as scaffolds" optional="False" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
        <test>
            <param name="name" value="12Gv1.0"/>
            <param name="description" value="12 plant genomes (Monocots, version 1.0)"/>
            <param name="web_url" value="https://github.com/gregvonkuster/galaxy_tools/raw/master/test/plant_tribes/scaffolds/12Gv1.0.tar.bz2"/>
            <param name="config_web_url" value="http://bigdata.bx.psu.edu/PlantTribes_scaffolds/configs/12Gv1.0.tar.gz"/>
            <output name="out_file" value="plant_tribes_scaffolds.json" compare="contains"/>
        </test>
    </tests>
    <help>
.. class:: infomark

**What it does**

This tool fetches scaffolds data and default configuration files used by the PlantTribes Galaxy tools and populates the
plant_tribes_scaffolds data table.  Both the scaffolds data and the default configuration files can be imported using a
URL, and an optional description can be provided that will appear next to the scaffolds file name in the data table entry.

Scaffolds data provided by the Floral Genome Project can be downloaded using these URLs:

 * 22 plant genomes (Angiosperms clusters, version 1.0):        http://bigdata.bx.psu.edu/PlantTribes_scaffolds/data/22Gv1.0.tar.bz2
 * 22 plant genomes (Angiosperms clusters, version 1.1):        http://bigdata.bx.psu.edu/PlantTribes_scaffolds/data/22Gv1.1.tar.bz2

Default configuration files provided by the Floral Genome Project can be downloaded using these URLs:

 * 22 plant genomes (Angiosperms clusters, version 1.0):        http://bigdata.bx.psu.edu/PlantTribes_scaffolds/configs/22Gv1.0.tar.gz
 * 22 plant genomes (Angiosperms clusters, version 1.1):        http://bigdata.bx.psu.edu/PlantTribes_scaffolds/configs/22Gv1.1.tar.gz
 
    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {Greg Von Kuster},
            title = {None},
            year = {None},
            eprint = {None},
            url = {https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader}
        }</citation>
    </citations>
</tool>