Mercurial > repos > iuc > data_manager_fetch_busco

annotate data_manager/busco_fetcher.xml @ 4:171e112d2030 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
author iuc
date Thu, 20 Feb 2025 20:14:32 +0000
parents 55e6b046a112
children e599b8e14cbd
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55e6b046a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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1 <tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
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2 <description>dataset dowloader</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">5.8.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
55e6b046a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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9 </requirements>
55e6b046a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2d2c72dc464b938bfa4def2511ce0938f3a1ea7d
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10 <command detect_errors="exit_code"><![CDATA[
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11 mkdir '$out_file.extra_files_path' &&
171e112d2030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
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12 busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
171e112d2030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
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13 cp '$dmjson' '$out_file'
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14 ]]></command>
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15 <configfiles>
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16 <configfile name="dmjson"><![CDATA[
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17 #from datetime import datetime
171e112d2030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
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18 {
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19 "data_tables":{
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20 "busco_database":[
171e112d2030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
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21 {
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22 "value":"$lineage #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
171e112d2030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
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23 "name":"$lineage #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
171e112d2030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
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24 "version":"@TOOL_VERSION@",
171e112d2030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
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25 "path":"$out_file.extra_files_path"
171e112d2030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 688b85175eeaf9b7790d4d7f337cbfb7d3dfde30
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26 }
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27 ]
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28 }
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29 }]]>
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30 </configfile>
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31 </configfiles>
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32 <inputs>
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33 <param name="lineage" type="select" label="Select the lineage to be downloaded">
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34 <option value="all">All</option>
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35 <option value="prokaryota">Prokaryota</option>
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36 <option value="eukaryota">Eukaryota</option>
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37 <option value="virus">Virus</option>
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38 </param>
f799082cbe53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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39 </inputs>
f799082cbe53 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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40 <outputs>
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41 <data name="out_file" format="data_manager_json" label="BUSCO data manager: JSON"/>
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42 </outputs>
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43 <tests>
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44 <test expect_num_outputs="1">
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45 <param name="lineage" value="virus"/>
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46 <output name="out_file">
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47 <assert_contents>
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48 <has_text text="virus"/>
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49 <has_text text="5.8.0"/>
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help>This tool downloads the BUSCO databases.</help>
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55 <citations>
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56 <citation type="doi">10.1093/bioinformatics/btv351</citation>
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57 </citations>
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58 </tool>