Mercurial > repos > iuc > data_manager_plant_tribes_scaffolds_downloader
annotate data_manager/data_manager_plant_tribes_scaffolds_download.xml @ 6:898b956719ee draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit a54e50916ebdb0858b049cdc549a43df801e1a71
author | iuc |
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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
iuc
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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"> |
0 | 2 <description></description> |
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93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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3 <requirements> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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4 <requirement type="package" version="3.8.3">python</requirement> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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5 </requirements> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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6 <command detect_errors="exit_code"><![CDATA[ |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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7 python $__tool_directory__/data_manager_plant_tribes_scaffolds_download.py |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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8 --name '$name' |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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9 --description '$description' |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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10 --web_url '$web_url' |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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11 --config_web_url '$config_web_url' |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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12 --out_file '$out_file']]> |
0 | 13 </command> |
14 <inputs> | |
15 <param name="name" type="text" value="" label="Data table entry unique ID"/> | |
16 <param name="description" type="text" value="" label="Description of the data" help="Value is optional"/> | |
2 | 17 <param name="web_url" type="text" value="" label="URL for downloading scaffolds" help="Must be same version as configs" optional="False" /> |
18 <param name="config_web_url" type="text" value="" label="URL for downloading configs" help="Must be same version as scaffolds" optional="False" /> | |
0 | 19 </inputs> |
20 <outputs> | |
21 <data name="out_file" format="data_manager_json" /> | |
22 </outputs> | |
23 <tests> | |
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93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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24 <test> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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25 <param name="name" value="12Gv1.0"/> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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26 <param name="description" value="12 plant genomes (Monocots, version 1.0)"/> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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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"/> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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28 <param name="config_web_url" value="http://bigdata.bx.psu.edu/PlantTribes_scaffolds/configs/12Gv1.0.tar.gz"/> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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29 <output name="out_file" value="plant_tribes_scaffolds.json" compare="contains"/> |
93253aebaf2e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 6085b7d47fcb47ad1587ac2542abdef782f61fe4"
iuc
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30 </test> |
0 | 31 </tests> |
32 <help> | |
33 .. class:: infomark | |
34 | |
35 **What it does** | |
36 | |
2 | 37 This tool fetches scaffolds data and default configuration files used by the PlantTribes Galaxy tools and populates the |
38 plant_tribes_scaffolds data table. Both the scaffolds data and the default configuration files can be imported using a | |
39 URL, and an optional description can be provided that will appear next to the scaffolds file name in the data table entry. | |
40 | |
41 Scaffolds data provided by the Floral Genome Project can be downloaded using these URLs: | |
0 | 42 |
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5833ef61c1f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 3b27dae566cb21e08f5915ae20e0727f7d694707
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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 |
5833ef61c1f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 3b27dae566cb21e08f5915ae20e0727f7d694707
iuc
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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 |
0 | 45 |
2 | 46 Default configuration files provided by the Floral Genome Project can be downloaded using these URLs: |
47 | |
3
5833ef61c1f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 3b27dae566cb21e08f5915ae20e0727f7d694707
iuc
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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 |
5833ef61c1f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader commit 3b27dae566cb21e08f5915ae20e0727f7d694707
iuc
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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 |
2 | 50 |
0 | 51 </help> |
52 <citations> | |
53 <citation type="bibtex"> | |
54 @unpublished{None, | |
55 author = {Greg Von Kuster}, | |
56 title = {None}, | |
57 year = {None}, | |
58 eprint = {None}, | |
2 | 59 url = {https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_plant_tribes_scaffolds_downloader} |
0 | 60 }</citation> |
61 </citations> | |
62 </tool> |