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1 <tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.1.0" 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 --config_web_url '$config_web_url'
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14 --out_file '$out_file'
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="name" type="text" value="" label="Data table entry unique ID"/>
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19 <param name="description" type="text" value="" label="Description of the data" help="Value is optional"/>
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20 <param name="web_url" type="text" value="" label="URL for downloading scaffolds" help="Must be same version as configs" optional="False" />
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21 <param name="config_web_url" type="text" value="" label="URL for downloading configs" help="Must be same version as scaffolds" optional="False" />
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22 </inputs>
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23 <outputs>
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24 <data name="out_file" format="data_manager_json" />
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25 </outputs>
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26 <tests>
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27 </tests>
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28 <help>
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29 .. class:: infomark
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30
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31 **What it does**
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32
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33 This tool fetches scaffolds data and default configuration files used by the PlantTribes Galaxy tools and populates the
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34 plant_tribes_scaffolds data table. Both the scaffolds data and the default configuration files can be imported using a
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35 URL, and an optional description can be provided that will appear next to the scaffolds file name in the data table entry.
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36
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37 Scaffolds data provided by the Floral Genome Project can be downloaded using these URLs:
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38
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39 * 22 plant genomes (Angiosperms clusters, version 1.0): http://fgp.huck.psu.edu/planttribes_data/22Gv1.0.tar.bz2
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40 * 22 plant genomes (Angiosperms clusters, version 1.1): http://fgp.huck.psu.edu/planttribes_data/22Gv1.1.tar.bz2
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41
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42 Default configuration files provided by the Floral Genome Project can be downloaded using these URLs:
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43
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44 * 22 plant genomes (Angiosperms clusters, version 1.0): http://fgp.huck.psu.edu/planttribes_config/22Gv1.0.tar.gz
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45 * 22 plant genomes (Angiosperms clusters, version 1.1): http://fgp.huck.psu.edu/planttribes_config/22Gv1.1.tar.gz
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46
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47 </help>
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48 <citations>
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49 <citation type="bibtex">
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50 @unpublished{None,
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51 author = {Greg Von Kuster},
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52 title = {None},
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53 year = {None},
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54 eprint = {None},
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55 url = {https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader}
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56 }</citation>
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57 </citations>
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58 </tool>
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