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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
author iuc
date Fri, 07 Mar 2025 22:33:29 +0000
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5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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1 <tool id="data_manager_funannotate_options" name="Funannotate options data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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2 <macros>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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3 <token name="@TOOL_VERSION@">1.8.15</token>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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4 <token name="@VERSION_SUFFIX@">0</token>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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5 </macros>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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6 <requirements>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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7 <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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8 </requirements>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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9 <version_command>funannotate check --show-versions</version_command>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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10 <command detect_errors="exit_code"><![CDATA[
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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11 #if $test:
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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12 funannotate setup -d ./test/ -i busco busco_outgroups -b eukaryota > /dev/null &&
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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13 #set db_path="./test"
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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14 #else
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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15 #set db_path=$database.fields.path
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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16 #end if
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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17 python '$__tool_directory__/extract.py' '$db_path' '$database' '$output_file'
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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18 ]]></command>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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19 <inputs>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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20 <param name="test" type="hidden" value="" help="Used for testing"/>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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21 <param name="database" label="Funannotate database" type="select">
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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22 <options from_data_table="funannotate">
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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23 <column name="value" index="0" />
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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24 <column name="name" index="1" />
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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25 <column name="path" index="3" />
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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26 <filter type="sort_by" column="0" reverse_sort_order="true"/>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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27 <!-- <filter type="static_value" column="2" value="1.0" /> -->
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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28 </options>
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29 </param>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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30 </inputs>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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31 <outputs>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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32 <data name="output_file" format="data_manager_json"/>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="test" value="true"/>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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37 <param name="database" value="test"/>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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38 <output name="output_file">
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39 <assert_contents>
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40 <has_text text="busco_db" n="1"/>
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41 <has_text text="outgroup" n="6"/>
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42 <has_text text="trained_species" n="166"/>
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43 </assert_contents>
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44 </output>
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45 <assert_stdout>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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46 <has_line line="1 x busco_db"/>
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47 <has_line line="166 x trained_species"/>
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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48 <has_line line="6 x outgroup"/>
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49 </assert_stdout>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53 This data managers determines the options available in the select parameters of the funannotate tool
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54 for a given funannotate DB in the funannotate data table
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55
5459ec34767a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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56 .. _funannotate: https://funannotate.readthedocs.io
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57 ]]></help>
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58 <citations>
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59 <citation type="doi">10.5281/zenodo.4054262</citation>
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60 </citations>
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61 </tool>