Mercurial > repos > iuc > data_manager_build_bracken_database

annotate data_manager/bracken_build_database.xml @ 5:cef566388a0f 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 db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
author iuc
date Mon, 22 May 2023 19:24:06 +0000
parents 66055e6b3cdf
children a0f18c07696a
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0891b7492a3c "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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1 <?xml version="1.0"?>
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cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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2 <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>bracken database builder</description>
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4 <macros>
cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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5 <token name="@TOOL_VERSION@">2.8</token>
cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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6 <token name="@VERSION_SUFFIX@">0</token>
cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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7 <token name="@PROFILE@">22.01</token>
cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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8 </macros>
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9 <requirements>
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cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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10 <requirement type="package" version="@TOOL_VERSION@">bracken</requirement>
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11 </requirements>
0891b7492a3c "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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12 <command>
0891b7492a3c "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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13 <![CDATA[
1
b980e034a6df "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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14 #import os
b980e034a6df "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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15 #set db_dir = os.path.basename($kraken_db.fields.path)
b980e034a6df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
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b980e034a6df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
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17 mkdir '$db_dir' &&
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18 ln -s '${kraken_db.fields.path}/*' '$db_dir/' &&
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19 python '$__tool_directory__/bracken_build_database.py'
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20 '${out_file}'
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21
0
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22 --threads \${GALAXY_SLOTS:-1}
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23 #if $check_prebuilt.prebuilt == "no"
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24 --kraken-db '$db_dir'
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25 --kmer-len ${check_prebuilt.kmer_len}
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26 #end if
66055e6b3cdf "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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27 #if $check_prebuilt.prebuilt == "yes"
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
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28 --kraken-db '${kraken_db.fields.path}'
66055e6b3cdf "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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29 --prebuilt
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30 #end if
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31 --read-len ${check_prebuilt.read_len}
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32 --database-name '${database_name}'
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33 ]]>
0891b7492a3c "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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34 </command>
0891b7492a3c "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 <inputs>
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36 <param name="kraken_db" type="select">
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37 <options from_data_table="kraken2_databases">
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38 <validator type="no_options" message="No Kraken2 databases are available" />
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39 </options>
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40 </param>
3
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41 <conditional name="check_prebuilt">
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42 <param name="prebuilt" type="select" label="Use Pre-built DB">
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43 <option value="no">No</option>
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44 <option value="yes">Yes</option>
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45 </param>
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46 <when value="no">
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47 <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" />
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48 <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" />
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49 </when>
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50 <when value="yes">
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51 <param name="read_len" type="select" label="Read length" >
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52 <option value="50">50</option>
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53 <option value="75">75</option>
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54 <option value="100" selected="true">100</option>
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55 <option value="150">150</option>
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56 <option value="200">200</option>
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57 <option value="250">250</option>
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58 <option value="300">300</option>
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59 </param>
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60 </when>
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61 </conditional>
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62 <param name="database_name" type="text" label="Database Name" />
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63 </inputs>
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64 <outputs>
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65 <data name="out_file" format="data_manager_json" />
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="kraken_db" value="test_entry" />
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70 <param name="database_name" value="database" />
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71 <output name="out_file">
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72 <assert_contents>
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73 <has_text text="test_db/database100mers.kmer_distrib" />
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74 </assert_contents>
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75 </output>
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76 </test>
0891b7492a3c "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 </tests>
0891b7492a3c "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 <help>
0891b7492a3c "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 </help>
0891b7492a3c "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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parents:
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80 <citations>
0891b7492a3c "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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parents:
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81 <citation type="doi">10.7717/peerj-cs.104</citation>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
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82 </citations>
0891b7492a3c "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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83 </tool>