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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit a54e50916ebdb0858b049cdc549a43df801e1a71
author iuc
date Tue, 21 May 2024 07:36:35 +0000
parents 93253aebaf2e
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898b956719ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit a54e50916ebdb0858b049cdc549a43df801e1a71
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1 <tool id="data_manager_plant_tribes_scaffolds_download" name="PlantTribes Scaffolds Download" version="1.1.2" tool_type="manage_data" profile="23.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="3.8.3">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py
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8 --name '$name'
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9 --description '$description'
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10 --web_url '$web_url'
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11 --config_web_url '$config_web_url'
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12 --out_file '$out_file']]>
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13 </command>
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14 <inputs>
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15 <param name="name" type="text" value="" label="Data table entry unique ID"/>
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16 <param name="description" type="text" value="" label="Description of the data" help="Value is optional"/>
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17 <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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18 <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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19 </inputs>
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20 <outputs>
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21 <data name="out_file" format="data_manager_json" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="name" value="12Gv1.0"/>
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26 <param name="description" value="12 plant genomes (Monocots, version 1.0)"/>
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27 <param name="web_url" value="https://github.com/gregvonkuster/galaxy_tools/raw/master/test/plant_tribes/scaffolds/12Gv1.0.tar.bz2"/>
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28 <param name="config_web_url" value="http://bigdata.bx.psu.edu/PlantTribes_scaffolds/configs/12Gv1.0.tar.gz"/>
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29 <output name="out_file" value="plant_tribes_scaffolds.json" compare="contains"/>
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30 </test>
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31 </tests>
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32 <help>
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33 .. class:: infomark
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34
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35 **What it does**
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36
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37 This tool fetches scaffolds data and default configuration files used by the PlantTribes Galaxy tools and populates the
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38 plant_tribes_scaffolds data table. Both the scaffolds data and the default configuration files can be imported using a
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39 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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40
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41 Scaffolds data provided by the Floral Genome Project can be downloaded using these URLs:
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42
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43 * 22 plant genomes (Angiosperms clusters, version 1.0): http://bigdata.bx.psu.edu/PlantTribes_scaffolds/data/22Gv1.0.tar.bz2
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44 * 22 plant genomes (Angiosperms clusters, version 1.1): http://bigdata.bx.psu.edu/PlantTribes_scaffolds/data/22Gv1.1.tar.bz2
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45
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46 Default configuration files provided by the Floral Genome Project can be downloaded using these URLs:
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47
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48 * 22 plant genomes (Angiosperms clusters, version 1.0): http://bigdata.bx.psu.edu/PlantTribes_scaffolds/configs/22Gv1.0.tar.gz
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49 * 22 plant genomes (Angiosperms clusters, version 1.1): http://bigdata.bx.psu.edu/PlantTribes_scaffolds/configs/22Gv1.1.tar.gz
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50
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51 </help>
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52 <citations>
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53 <citation type="bibtex">
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54 @unpublished{None,
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55 author = {Greg Von Kuster},
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56 title = {None},
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57 year = {None},
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58 eprint = {None},
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59 url = {https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader}
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60 }</citation>
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61 </citations>
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62 </tool>