Mercurial > repos > iuc > data_manager_funannotate
annotate data_manager/funannotate.xml @ 2:13018941c6a0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
author | iuc |
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date | Fri, 19 Nov 2021 11:15:54 +0000 |
parents | 8dff71edbce5 |
children | 0cadd0a04412 |
rev | line source |
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2
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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1 <tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01"> |
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ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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2 <requirements> |
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8dff71edbce5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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3 <requirement type="package" version="1.8.9">funannotate</requirement> |
8dff71edbce5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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4 <requirement type="package" version="2.26.0">requests</requirement> |
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ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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5 </requirements> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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6 <version_command>funannotate check --show-versions</version_command> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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7 <command detect_errors="exit_code"><![CDATA[ |
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8dff71edbce5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
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8 python -u '$__tool_directory__/funannotate.py' |
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ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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9 $partial_data |
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13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
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10 $wget |
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ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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11 \$(date +'%Y-%m-%d-%H%M%S') |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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12 'funannotate' |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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13 '${output_file}' |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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14 ]]></command> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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15 <inputs> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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16 <param name="partial_data" type="hidden" value="" help="Used for testing"/> |
2
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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17 <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/> |
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ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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18 </inputs> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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19 <outputs> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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20 <data name="output_file" format="data_manager_json"/> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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21 </outputs> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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22 <tests> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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23 <test> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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24 <param name="partial_data" value="--partial"/> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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25 <output name="output_file"> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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26 <assert_contents> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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27 <has_text text="Funannotate database "/> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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28 <has_text text='"format_version": "1.0"'/> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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29 </assert_contents> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
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30 </output> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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31 </test> |
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13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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32 <test> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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33 <param name="partial_data" value="--partial"/> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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34 <param name="wget" value="True"/> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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35 <output name="output_file"> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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36 <assert_contents> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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37 <has_text text="Funannotate database "/> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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38 <has_text text='"format_version": "1.0"'/> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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39 </assert_contents> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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40 </output> |
13018941c6a0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
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41 </test> |
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ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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42 </tests> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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43 <help><![CDATA[ |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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44 This data managers fetches data from various databases for the funannotate |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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45 annotation tool and updates the funannotate data table. |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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46 |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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47 .. _funannotate: https://funannotate.readthedocs.io |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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48 ]]></help> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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49 <citations> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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50 <citation type="doi">10.5281/zenodo.4054262</citation> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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51 </citations> |
ef7f9e2f32f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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52 </tool> |