Mercurial > repos > iuc > data_manager_build_bracken_database

annotate data_manager/bracken_build_database.xml @ 3:3c7d2c84cb09 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
author iuc
date Mon, 08 Nov 2021 15:51:51 +0000
parents 9059edc96a85
children 5c8a23ccb14a
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1 <?xml version="1.0"?>
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2 <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy1" profile="19.01">
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3 <description>bracken database builder</description>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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4 <requirements>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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5 <requirement type="package" version="2.5">bracken</requirement>
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3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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6 <requirement type="package" version="2.1.1">kraken2</requirement>
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7 </requirements>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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8 <command>
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9 <![CDATA[
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9059edc96a85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
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10 #import os
9059edc96a85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
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11 #set db_dir = os.path.basename($kraken_db.fields.path)
9059edc96a85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
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9059edc96a85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
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13 mkdir '$db_dir' &&
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14 ln -s '${kraken_db.fields.path}/*' '$db_dir/' &&
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15 python '$__tool_directory__/bracken_build_database.py'
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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16 '${out_file}'
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17
0
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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18 --threads \${GALAXY_SLOTS:-1}
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19 #if $check_prebuilt.prebuilt == "no"
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20 --kraken-db '$db_dir'
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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21 --kmer-len ${check_prebuilt.kmer_len}
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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22 #end if
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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23 #if $check_prebuilt.prebuilt == "yes"
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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24 --kraken-db '${kraken_db.fields.path}'
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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25 --prebuilt
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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26 #end if
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27 --read-len ${check_prebuilt.read_len}
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28 --database-name '${database_name}'
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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29 ]]>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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30 </command>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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31 <inputs>
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32 <param name="kraken_db" type="select">
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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33 <options from_data_table="kraken2_databases">
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34 <validator type="no_options" message="No Kraken2 databases are available" />
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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35 </options>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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36 </param>
3
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37 <conditional name="check_prebuilt">
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38 <param name="prebuilt" type="select" label="Use Pre-built DB">
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39 <option value="no">No</option>
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40 <option value="yes">Yes</option>
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41 </param>
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42 <when value="no">
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43 <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" />
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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44 <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" />
3c7d2c84cb09 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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45 </when>
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46 <when value="yes">
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47 <param name="read_len" type="select" label="Read length" >
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48 <option value="50">50</option>
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49 <option value="75">75</option>
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50 <option value="100">100</option>
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51 <option value="150">150</option>
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52 <option value="200">200</option>
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53 <option value="250">250</option>
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54 <option value="300">300</option>
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55 </param>
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56 </when>
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57 </conditional>
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58 <param name="database_name" type="text" label="Database Name" />
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59 </inputs>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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60 <outputs>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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61 <data name="out_file" format="data_manager_json" />
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62 </outputs>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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63 <tests>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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64 <test>
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65 <param name="kraken_db" value="test_entry" />
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66 <param name="database_name" value="database" />
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67 <output name="out_file">
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68 <assert_contents>
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69 <has_text text="test_db/database100mers.kmer_distrib" />
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70 </assert_contents>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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71 </output>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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72 </test>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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73 </tests>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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74 <help>
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75 </help>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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76 <citations>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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77 <citation type="doi">10.7717/peerj-cs.104</citation>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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78 </citations>
c2e4127fb5bf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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79 </tool>