annotate data_manager/omamer.xml @ 2:f8d72275878e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
author iuc
date Wed, 14 Aug 2024 15:42:46 +0000
parents 57db282ca204
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57db282ca204 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
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1 <tool id="data_manager_omamer" name="OMAmer data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
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2 <macros>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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3 <import>macros.xml</import>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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4 </macros>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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5 <version_command></version_command>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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6 <command detect_errors="exit_code"><![CDATA[
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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7 python '$__tool_directory__/omamer.py'
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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8 --name '$name'
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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9 --json '$output_file'
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57db282ca204 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
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10 --version '@TOOL_VERSION@'
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e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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11 ]]></command>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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12 <inputs>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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13 <param name="output_dir" type="text" label="Output Directory" value=""/>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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14 <param name="name" type="select" label="Database">
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f8d72275878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
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15 <option value="Primates_v2.0.0">Primates_v2.0.0</option>
f8d72275878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
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16 <option value="Viridiplantae_v2.0.0">Viridiplantae_v2.0.0</option>
f8d72275878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
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17 <option value="Metazoa_v2.0.0">Metazoa_v2.0.0</option>
f8d72275878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
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18 <option value="LUCA_v0.2.5">LUCA_v0.2.5</option>
f8d72275878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
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19 <option value="LUCA_v2.0.0">LUCA_v2.0.0</option>
f8d72275878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
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20 <option value="Saccharomyceta">Saccharomyceta</option>
f8d72275878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
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21 <option value="Homininae">Homininae</option>
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e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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22 </param>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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23 </inputs>
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24
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25 <outputs>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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26 <data name="output_file" format="data_manager_json" label="OMAmer data manager: JSON"/>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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27 </outputs>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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29 <tests>
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30 <test>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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31 <param name="output_dir" value="test_galaxy"/>
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f8d72275878e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
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32 <param name="name" value="Primates_v2.0.0"/>
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33 <output name="output_file" file="out.json"/>
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34 </test>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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35 </tests>
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36
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37 <help><![CDATA[
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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38 This data manager retrieves data from various pre-built databases.
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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39
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40 .. _omamer: https://github.com/DessimozLab/omamer
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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41 ]]></help>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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42 <citations>
e1502e4f8725 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
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43 <citation type="doi">10.1093/bioinformatics/btab219</citation>
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44 </citations>
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45 </tool>