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1 <tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.0.0" tool_type="manage_data">
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2 <description></description>
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3 <stdio>
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4 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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5 <exit_code range="1:" level="fatal" description="Error" />
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6 </stdio>
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7 <command>
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8 <![CDATA[
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9 python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py
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10 --name "$name"
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11 --description "$description"
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12 --web_url "$web_url"
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13 --out_file "$out_file"
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="name" type="text" value="" label="Data table entry unique ID"/>
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18 <param name="description" type="text" value="" label="Description of the data" help="Value is optional"/>
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19 <param name="web_url" type="text" value="" label="Web URL" optional="False" />
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20 </inputs>
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21 <outputs>
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22 <data name="out_file" format="data_manager_json" />
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23 </outputs>
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24 <tests>
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25 </tests>
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26 <help>
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27 .. class:: infomark
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28
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29 **What it does**
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30
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31 This tool fetches scaffolds data used by the PlantTribes Galaxy tools and populates the plant_tribes_scaffolds data table.
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32 The scaffolds data can be imported using a URL, and an optional description can be provided that will appear next to the
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33 scaffolds file name in the data table entry. Scaffolds data provided by the Floral Genome Project can be downloaded here:
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34
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35 * 22 plant genomes (Angiosperms clusters, version 1.0): http://fgp.huck.psu.edu/planttribes_data/22Gv1.0.tar.bz2
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36 * 22 plant genomes (Angiosperms clusters, version 1.1): http://fgp.huck.psu.edu/planttribes_data/22Gv1.1.tar.bz2
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37
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38 </help>
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39 <citations>
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40 <citation type="bibtex">
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41 @unpublished{None,
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42 author = {Greg Von Kuster},
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43 title = {None},
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44 year = {None},
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45 eprint = {None},
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46 url = {None}
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47 }</citation>
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48 </citations>
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49 </tool>
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