view data_manager/data_manager_plant_tribes_scaffolds_download.xml @ 0:4c96b684f0fd draft

Uploaded

<tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.0.0" tool_type="manage_data">
    <description></description>
    <stdio>
        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:" level="fatal" description="Error" />
    </stdio>
    <command>
        <![CDATA[
            python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py
            --name "$name"
            --description "$description"
            --web_url "$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="Web URL" optional="False" />
    </inputs>
    <outputs>
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <tests>
    </tests>
    <help>
.. class:: infomark

**What it does**

This tool fetches scaffolds data used by the PlantTribes Galaxy tools and populates the plant_tribes_scaffolds data table.
The scaffolds data 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 here:

 * 22 plant genomes (Angiosperms clusters, version 1.0):        http://fgp.huck.psu.edu/planttribes_data/22Gv1.0.tar.bz2
 * 22 plant genomes (Angiosperms clusters, version 1.1):        http://fgp.huck.psu.edu/planttribes_data/22Gv1.1.tar.bz2

    </help>
    <citations>
        <citation type="bibtex">
            @unpublished{None,
            author = {Greg Von Kuster},
            title = {None},
            year = {None},
            eprint = {None},
            url = {None}
        }</citation>
    </citations>
</tool>