Mercurial > repos > iuc > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.xml @ 5:0d6cdde238ba draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
author iuc
date Mon, 08 Nov 2021 15:40:07 +0000
parents 5f4b0a3cb38b
children 691a1055a112
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a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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1 <?xml version="1.0"?>
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5f4b0a3cb38b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@" profile="18.09">
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a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.1.1</token>
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a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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5 <xml name="common_params">
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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6 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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7 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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8 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
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9 <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
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10 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
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11 </xml>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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12 </macros>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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13 <description>database builder</description>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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14 <requirements>
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15 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
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16 <requirement type="package" version="3.7">python</requirement>
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17 </requirements>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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18 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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19 <command detect_errors="exit_code">
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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20 <![CDATA[
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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21 python '$__tool_directory__/kraken2_build_database.py'
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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22 '${out_file}'
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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23 --database-type ${database_type.database_type}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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24 #if $database_type.database_type == "minikraken"
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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25 --minikraken2-version ${database_type.minikraken2_version}
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0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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26 #else if $database_type.database_type == "standard_prebuilt"
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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27 --standard-prebuilt-size ${database_type.standard_prebuilt_size}
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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28 #if $database_type.prebuilt_date_custom != ""
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29 --prebuilt-date ${database_type.prebuilt_date_custom}
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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30 #else
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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31 --prebuilt-date ${database_type.prebuilt_date}
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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32 #end if
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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33 #else if $database_type.database_type == "standard_local_build"
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34 --threads \${GALAXY_SLOTS:-1}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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35 --kmer-len ${database_type.kmer_len}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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36 --minimizer-len ${database_type.minimizer_len}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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37 --minimizer-spaces ${database_type.minimizer_spaces}
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38 --load-factor ${database_type.load_factor}
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39 ${database_type.clean}
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40 #else if $database_type.database_type == "special"
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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41 --threads \${GALAXY_SLOTS:-1}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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42 --special-database-type ${database_type.special_database_type}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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43 --kmer-len ${database_type.kmer_len}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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44 --minimizer-len ${database_type.minimizer_len}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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45 --minimizer-spaces ${database_type.minimizer_spaces}
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46 --load-factor ${database_type.load_factor}
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47 ${database_type.clean}
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48 #else if $database_type.database_type == "custom"
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49 --threads \${GALAXY_SLOTS:-1}
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50 ${database_type.skip_maps}
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51 --custom-fasta ${database_type.custom_fasta}
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52 --custom-database-name ${database_type.custom_database_name}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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53 --kmer-len ${database_type.kmer_len}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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54 --minimizer-len ${database_type.minimizer_len}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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55 --minimizer-spaces ${database_type.minimizer_spaces}
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56 --load-factor ${database_type.load_factor}
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57 ${database_type.clean}
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58 #end if
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59 ]]>
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60 </command>
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61 <inputs>
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62 <conditional name="database_type">
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63 <param name="database_type" type="select" multiple="false" label="Database Type">
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64 <option value="standard_local_build">Standard, Local Build</option>
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65 <option value="standard_prebuilt">Standard, Pre-Built</option>
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66 <option value="minikraken">MiniKraken</option>
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67 <option value="special">Special</option>
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68 <option value="custom">Custom</option>
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69 </param>
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70 <when value="standard_local_build">
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71 <expand macro="common_params" />
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72 </when>
5
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73 <when value="standard_prebuilt">
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74 <param name="standard_prebuilt_size" type="select" multiple="false" label="Select size of prebuilt database to download">
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75 <option value="full">Standard-Full (~50 GB)</option>
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76 <option value="16">Standard-16 (~16 GB)</option>
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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77 <option value="8">Standard-8 (~8 GB)</option>
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78 </param>
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79 <param name="prebuilt_date" type="select" multiple="false" optional="true" label="Select database build date">
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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80 <option value="2021-05-17">May 17, 2021</option>
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81 <option value="2020-12-02">December 2, 2020</option>
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82 </param>
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83 <param name="prebuilt_date_custom" type="text" label="Custom date (YYYY-MM-DD)" help="Any text here will overwrite the selected date above." />
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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84 </when>
0
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85 <when value="minikraken">
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86 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
1
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87 <option value="v2">Version 2</option>
0
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88 <option value="v1">Version 1</option>
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89 </param>
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90 </when>
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91 <when value="special">
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92 <param name="special_database_type" type="select" multiple="false" label="Select database to build">
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93 <option value="greengenes">Greengenes</option>
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94 <option value="silva">Silva</option>
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95 <option value="rdp">RDP</option>
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96 </param>
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97 <expand macro="common_params" />
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98 </when>
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99 <when value="custom">
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100 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
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101 <param name="custom_database_name" type="text" label="Name for this database" />
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102 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
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103 <expand macro="common_params" />
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104 </when>
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105 </conditional>
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106 </inputs>
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107 <outputs>
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108 <data name="out_file" format="data_manager_json" />
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109 </outputs>
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110 <tests>
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111 <test>
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112 <param name="database_type" value="custom" />
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113 <param name="custom_fasta" value="adapter.fa" />
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114 <param name="custom_database_name" value="database" />
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115 <param name="skip_maps" value="true" />
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116 <output name="out_file" value="kraken2_custom_data_manager.json" />
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117 </test>
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118 </tests>
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119 <help>
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120 </help>
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121 <citations>
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122 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
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123 </citations>
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124 </tool>