Mercurial > repos > iuc > data_manager_funannotate

annotate data_manager/funannotate.xml @ 1:8dff71edbce5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
author iuc
date Thu, 18 Nov 2021 21:55:43 +0000
parents ef7f9e2f32f2
children 13018941c6a0
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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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1 <tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.2" 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"
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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"
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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"
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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"
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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"
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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"
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9 $partial_data
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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10 \$(date +'%Y-%m-%d-%H%M%S')
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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11 'funannotate'
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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12 '${output_file}'
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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13 ]]></command>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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14 <inputs>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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15 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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16 </inputs>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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17 <outputs>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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18 <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"
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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"
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20 <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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21 <test>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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22 <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"
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23 <output name="output_file">
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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24 <assert_contents>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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25 <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"
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26 <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"
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27 </assert_contents>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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28 </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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29 </test>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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30 </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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31 <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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32 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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33 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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34
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
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35 .. _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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36 ]]></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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37 <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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38 <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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39 </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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40 </tool>