Mercurial > repos > iuc > data_manager_fetch_busco

annotate data_manager/busco_fetcher.xml @ 8:29548c43fb33 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
author iuc
date Tue, 22 Apr 2025 13:11:38 +0000
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29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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1 <tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.1">
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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2 <description>dataset dowloader</description>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
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3 <macros>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
iuc
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4 <token name="@TOOL_VERSION@">5.8.0</token>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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5 <token name="@VERSION_SUFFIX@">1</token>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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6 </macros>
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iuc
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7 <requirements>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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8 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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9 </requirements>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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10 <command detect_errors="exit_code"><![CDATA[
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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11 busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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12 ## remove unwanted lineage folders and placement files
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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13 ## https://gitlab.com/ezlab/busco/-/issues/784
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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14 if [ -d '$out_file.extra_files_path'/lineages ]; then
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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15 find '$out_file.extra_files_path'/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -exec rm -rf {} \;;
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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16 fi &&
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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17 if [ -d '$out_file.extra_files_path'/placement_files ]; then
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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18 find '$out_file.extra_files_path'/placement_files/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -delete;
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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19 fi &&
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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20 ## unpack faa.gz files ready to use
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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21 ## https://gitlab.com/ezlab/busco/-/issues/789
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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22 if [ -d '$out_file.extra_files_path'/lineages ]; then
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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23 find '$out_file.extra_files_path'/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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24 fi
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25 && cp '$dmjson' '$out_file'
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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26 ]]></command>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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27 <configfiles>
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28 <configfile name="dmjson"><![CDATA[
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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29 #from datetime import datetime
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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30 {
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31 "data_tables":{
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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32 "busco_database":[
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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33 {
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34 "value":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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35 "name":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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36 "version":"@TOOL_VERSION@",
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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37 "path":"$out_file.extra_files_path"
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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38 }
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39 ]
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40 }
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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41 }]]>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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42 </configfile>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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43 </configfiles>
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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44 <inputs>
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45 <param name="lineage" argument="--download" type="select" label="Select the lineage to be downloaded">
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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46 <option value="all">All</option>
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47 <option value="prokaryota">Prokaryota</option>
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48 <option value="eukaryota">Eukaryota</option>
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49 <option value="virus">Virus</option>
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50 </param>
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51 <param argument="--datasets_version" type="select" label="OrthoDB version" help="By March 2025 OrthoDB 12 datasets were only available for Prokaryota (https://busco-data2.ezlab.org/v5/data/)">
29548c43fb33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e
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52 <option value="odb10" selected="true">OrthoDB 10</option>
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53 <option value="odb12">OrthoDB 12</option>
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54 </param>
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55 </inputs>
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56 <outputs>
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57 <data name="out_file" format="data_manager_json" label="BUSCO data manager: JSON"/>
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58 </outputs>
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59 <tests>
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60 <test expect_num_outputs="1">
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61 <param name="lineage" value="virus"/>
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62 <output name="out_file">
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63 <assert_contents>
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64 <has_text text="virus"/>
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65 <has_text text="5.8.0"/>
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66 </assert_contents>
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67 </output>
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68 </test>
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69 </tests>
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70 <help>This tool downloads the BUSCO databases.</help>
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71 <citations>
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72 <citation type="doi">10.1093/bioinformatics/btv351</citation>
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73 </citations>
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74 </tool>