Mercurial > repos > iuc > data_manager_fetch_busco

annotate data_manager/busco_fetcher.xml @ 0:53eec20e8fb6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author iuc
date Thu, 19 Oct 2017 15:56:20 -0400
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53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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1 <?xml version="1.0"?>
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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2 <tool id="busco_fetcher" name="Busco" tool_type="manage_data" version="1.0.0">
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3 <description>dataset dowloader</description>
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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4 <command detect_errors="exit_code">
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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5 <![CDATA[
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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6 python '$__tool_directory__/data_manager.py' --out '${out_file}'
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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7 --url 'http://busco.ezlab.org/datasets/${dataset}.tar.gz'
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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8 --name '${dataset}'
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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9 ]]>
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10 </command>
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11 <inputs>
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12 <param name="dataset" type="select" label="Choose dataset to download">
53eec20e8fb6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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13 <option value="eukaryota_odb9">eukaryota</option>
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14 <option value="metazoa_odb9">metazoa</option>
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15 <option value="nematoda_odb9">nematoda</option>
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16 <option value="arthropoda_odb9">arthropoda</option>
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17 <option value="insecta_odb9">insecta</option>
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18 <option value="endopterygota_odb9">endopterygota</option>
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19 <option value="hymenoptera_odb9">hymenoptera</option>
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20 <option value="diptera_odb9">diptera</option>
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21 <option value="vertebrata_odb9">vertebrata</option>
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22 <option value="actinopterygii_odb9">actinopterygii</option>
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23 <option value="tetrapoda_odb9">tetrapoda</option>
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24 <option value="aves_odb9">aves</option>
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25 <option value="mammalia_odb9">mammalia</option>
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26 <option value="euarchontoglires_odb9">euarchontoglires</option>
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27 <option value="laurasiatheria_odb9">laurasiatheria</option>
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28 <option value="embryophyta_odb9">embryophyta</option>
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29 <option value="protists_ensembl">protists</option>
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30 <option value="alveolata_stramenophiles_ensembl">alveolata</option>
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31 <option value="fungi_odb9">fungi</option>
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32 <option value="microsporidia_odb9">microsporidia</option>
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33 <option value="dikarya_odb9">dikarya</option>
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34 <option value="ascomycota_odb9">ascomycota</option>
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35 <option value="pezizomycotina_odb9">pezizomycotina</option>
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36 <option value="eurotiomycetes_odb9">eurotiomycetes</option>
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37 <option value="sordariomyceta_odb9">sordariomyceta</option>
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38 <option value="saccharomyceta_odb9">saccharomyceta</option>
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39 <option value="saccharomycetales_odb9">saccharomycetales</option>
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40 <option value="basidiomycota_odb9">basidiomycota</option>
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41 <option value="bacteria_odb9">bacteria</option>
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42 <option value="proteobacteria_odb9">proteobacteria</option>
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43 <option value="rhizobiales_odb9">rhizobiales</option>
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44 <option value="betaproteobacteria_odb9">betaproteobacteria</option>
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45 <option value="gammaproteobacteria_odb9">gammaproteobacteria</option>
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46 <option value="enterobacteriales_odb9">enterobacteriales</option>
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47 <option value="deltaepsilonsub_odb9">deltaepsilonsub</option>
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48 <option value="actinobacteria_odb9">actinobacteria</option>
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49 <option value="cyanobacteria_odb9">cyanobacteria</option>
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50 <option value="firmicutes_odb9">firmicutes</option>
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51 <option value="clostridia_odb9">clostridia</option>
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52 <option value="lactobacillales_odb9">lactobacillales</option>
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53 <option value="bacillales_odb9">bacillales</option>
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54 <option value="bacteroidetes_odb9">bacteroidetes</option>
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55 <option value="spirochaetes_odb9">spirochaetes</option>
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56 <option value="tenericutes_odb9">tenericutes</option>
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57 </param>
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58 </inputs>
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59 <outputs>
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60 <data name="out_file" format="data_manager_json" />
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61 </outputs>
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62 </tool>