Mercurial > repos > iuc > data_manager_funannotate

annotate data_manager/funannotate.xml @ 4:10899aa247fc draft

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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 22:28:23 +0000
parents 83bd7b5eebfb
children
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4
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
iuc
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1 <tool id="data_manager_funannotate" name="Funannotate data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
iuc
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2 <macros>
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
iuc
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3 <token name="@TOOL_VERSION@">1.8.15</token>
10899aa247fc 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>
10899aa247fc 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>
0
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
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8 </requirements>
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9 <version_command>funannotate check --show-versions</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
4
10899aa247fc 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 $wget:
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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12 ## Asked for wget, we assume there's a certificate problem on (at least) one
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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13 ## of the many requested servers, force disable of all checks
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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14 echo "check_certificate = off" > \$HOME/.wgetrc &&
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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15 #end if
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16
4
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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17 funannotate setup
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18 -d '$output_file.extra_files_path'
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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19 #if $partial_data
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20 -i merops -b eukaryota
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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21 #else
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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22 -b all
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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23 #end if
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24 $wget
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25 &&
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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26 cp '$dmjson' '$output_file'
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27 ]]></command>
4
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28 <configfiles>
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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29 <configfile name="dmjson"><![CDATA[
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30 #from datetime import datetime
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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31 #set version_id=datetime.now().strftime("%Y-%m-%d-%H%M%S")
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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32 {
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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33 "data_tables":{
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34 "funannotate":[
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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35 {
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36 "value":"$version_id",
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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37 "description":"Funannotate database $version_id",
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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38 "format_version":"1.0",
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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39 "path":"$output_file.extra_files_path"
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40 }
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41 ]
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42 }
10899aa247fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4
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43 }]]></configfile>
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44 </configfiles>
0
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45 <inputs>
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46 <param name="partial_data" type="hidden" value="" help="Used for testing"/>
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47 <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
0
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48 </inputs>
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49 <outputs>
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50 <data name="output_file" format="data_manager_json"/>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="partial_data" value="--partial"/>
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55 <output name="output_file">
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56 <assert_contents>
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57 <has_text text="Funannotate database "/>
4
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58 <has_text text='"format_version":"1.0"'/>
0
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59 </assert_contents>
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60 </output>
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61 </test>
2
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62 <test>
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63 <param name="partial_data" value="--partial"/>
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64 <param name="wget" value="True"/>
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65 <output name="output_file">
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66 <assert_contents>
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67 <has_text text="Funannotate database "/>
4
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68 <has_text text='"format_version":"1.0"'/>
2
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69 </assert_contents>
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70 </output>
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71 </test>
0
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72 </tests>
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73 <help><![CDATA[
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74 This data managers fetches data from various databases for the funannotate
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75 annotation tool and updates the funannotate data table.
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76
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77 .. _funannotate: https://funannotate.readthedocs.io
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78 ]]></help>
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79 <citations>
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80 <citation type="doi">10.5281/zenodo.4054262</citation>
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81 </citations>
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82 </tool>