Mercurial > repos > iuc > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.xml @ 6:9002633b4737 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 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
author iuc
date Fri, 24 Jun 2022 12:44:33 +0000
parents 2f27f3b86827
children e4b4837f06f5
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e4cdf82de430 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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2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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e4cdf82de430 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>
6
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4 <token name="@TOOL_VERSION@">2.1.2</token>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">21.01</token>
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7 <xml name="common_params">
e4cdf82de430 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="kmer_len" type="integer" value="35" label="K-mer length in BP" />
e4cdf82de430 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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9 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
e4cdf82de430 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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10 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
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0eebe086fd58 "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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11 <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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12 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
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13 </xml>
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14 <xml name="viral">
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15 <option value="viral">Viral (viral; ~50 GB)</option>
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16 </xml>
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17 <xml name="minusb">
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18 <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
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19 </xml>
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20 <xml name="standard">
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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21 <option value="standard">Standard-Full (archaea, bacteria, viral, plasmid, human, UniVec_Core; ~50 GB)</option>
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22 </xml>
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23 <xml name="standard_08gb">
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24 <option value="standard_08gb">Standard-8 (Standard with DB capped at 8 GB)</option>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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25 </xml>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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26 <xml name="standard_16gb">
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27 <option value="standard_16gb">Standard-16 (Standard with DB capped at 16 GB)</option>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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28 </xml>
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29 <xml name="pluspf">
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30 <option value="pluspf">PlusPF (Standard plus protozoa and fungi; ~50 GB)</option>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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31 </xml>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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32 <xml name="pluspf_08gb">
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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33 <option value="pluspf_08gb">PlusPF-8 (PlusPF with DB capped at 8 GB; ~7.5 GB)</option>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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34 </xml>
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35 <xml name="pluspf_16gb">
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36 <option value="pluspf_16gb">PlusPF-16 (PlusPF with DB capped at 16 GB; ~15 GB)</option>
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37 </xml>
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38 <xml name="pluspfp">
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39 <option value="pluspfp">PlusPFP (Standard plus protozoa, fungi and plant; ~129 GB)</option>
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40 </xml>
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41 <xml name="pluspfp_08gb">
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42 <option value="pluspfp_08gb">PlusPFP-8 (PlusPFP with DB capped at 8 GB; ~7.5 GB)</option>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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43 </xml>
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44 <xml name="pluspfp_16gb">
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45 <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
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46 </xml>
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47 </macros>
e4cdf82de430 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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48 <description>database builder</description>
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49 <requirements>
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0eebe086fd58 "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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50 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
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edacc4bcd3cb "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 1c0a28222ac235e77b2a792c1ebca027a746c220"
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51 <requirement type="package" version="3.7">python</requirement>
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52 </requirements>
e4cdf82de430 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 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
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54 <command detect_errors="exit_code"><![CDATA[
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55 python '$__tool_directory__/kraken2_build_database.py'
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56 '$out_file'
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57 --database-type '$database_type.database_type'
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58 #if $database_type.database_type == "standard_local_build"
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59 --threads \${GALAXY_SLOTS:-1}
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60 --kmer-len $database_type.kmer_len
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61 --minimizer-len $database_type.minimizer_len
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62 --minimizer-spaces $database_type.minimizer_spaces
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63 --load-factor $database_type.load_factor
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64 $database_type.clean
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65 #else if $database_type.database_type == "standard_prebuilt"
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66 --prebuilt-db '$database_type.prebuild.prebuilt_db'
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67 --prebuilt-date '$database_type.prebuild.prebuilt_date'
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68 #else if $database_type.database_type == "minikraken"
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69 --minikraken2-version '$database_type.minikraken2_version'
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70 #else if $database_type.database_type == "special"
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71 --threads \${GALAXY_SLOTS:-1}
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72 --special-database-type '$database_type.special_database_type'
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73 --kmer-len $database_type.kmer_len
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74 --minimizer-len $database_type.minimizer_len
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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75 --minimizer-spaces $database_type.minimizer_spaces
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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76 --load-factor $database_type.load_factor
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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77 $database_type.clean
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78 #else if $database_type.database_type == "custom"
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79 --threads \${GALAXY_SLOTS:-1}
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80 --custom-fasta '$database_type.custom_fasta'
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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81 --custom-database-name '$database_type.custom_database_name'
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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82 $database_type.skip_maps
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83 --kmer-len $database_type.kmer_len
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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84 --minimizer-len $database_type.minimizer_len
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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85 --minimizer-spaces $database_type.minimizer_spaces
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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86 --load-factor $database_type.load_factor
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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87 $database_type.clean
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88 #end if
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89 ]]>
0
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90 </command>
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91 <inputs>
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92 <conditional name="database_type">
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93 <param name="database_type" type="select" multiple="false" label="Database Type">
5
2f27f3b86827 "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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94 <option value="standard_local_build">Standard, Local Build</option>
6
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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95 <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
0
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96 <option value="minikraken">MiniKraken</option>
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97 <option value="special">Special</option>
e4cdf82de430 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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98 <option value="custom">Custom</option>
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99 </param>
5
2f27f3b86827 "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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100 <when value="standard_local_build">
0
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101 <expand macro="common_params" />
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102 </when>
5
2f27f3b86827 "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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103 <when value="standard_prebuilt">
6
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104 <conditional name="prebuild">
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105 <param name="prebuilt_date" type="select" label="Select index build date">
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106 <option value="2022-06-07">June 7, 2022</option>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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107 <option value="2021-05-17">May 17, 2021</option>
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108 <option value="2021-01-27">January 27, 2021</option>
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109 <option value="2020-12-02">December 2, 2020</option>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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110 <option value="2020-09-19">September 19, 2020</option>
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111 </param>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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112 <when value="2022-06-07">
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113 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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114 <expand macro="viral"/>
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115 <expand macro="minusb"/>
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116 <expand macro="standard"/>
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117 <expand macro="standard_08gb"/>
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118 <expand macro="standard_16gb"/>
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119 <expand macro="pluspf"/>
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120 <expand macro="pluspf_08gb"/>
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121 <expand macro="pluspf_16gb"/>
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122 <expand macro="pluspfp"/>
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123 <expand macro="pluspfp_08gb"/>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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124 <expand macro="pluspfp_16gb"/>
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125 </param>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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126 </when>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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127 <when value="2021-05-17">
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128 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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129 <expand macro="viral"/>
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130 <expand macro="minusb"/>
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131 <expand macro="standard"/>
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132 <expand macro="standard_08gb"/>
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133 <expand macro="standard_16gb"/>
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134 <expand macro="pluspf"/>
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135 <expand macro="pluspf_08gb"/>
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diff changeset
136 <expand macro="pluspf_16gb"/>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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137 <expand macro="pluspfp_08gb"/>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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138 <expand macro="pluspfp_16gb"/>
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139 </param>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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140 </when>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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141 <when value="2021-01-27">
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142 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
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143 <expand macro="pluspf"/>
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diff changeset
144 <expand macro="pluspf_08gb"/>
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145 <expand macro="pluspf_16gb"/>
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146 <expand macro="pluspfp_08gb"/>
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147 <expand macro="pluspfp_16gb"/>
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148 </param>
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149 </when>
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iuc
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150 <when value="2020-12-02">
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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151 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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diff changeset
152 <expand macro="viral"/>
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iuc
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153 <expand macro="minusb"/>
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iuc
parents: 5
diff changeset
154 <expand macro="standard"/>
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iuc
parents: 5
diff changeset
155 <expand macro="standard_08gb"/>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
156 <expand macro="standard_16gb"/>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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157 </param>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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158 </when>
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iuc
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159 <when value="2020-09-19">
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160 <param name="prebuilt_db" type="select" multiple="false" label="Select a prebuilt Refseq indexes to download">
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
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diff changeset
161 <expand macro="minusb"/>
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162 <expand macro="standard"/>
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163 <expand macro="standard_08gb"/>
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iuc
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164 <expand macro="standard_16gb"/>
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165 <expand macro="pluspf"/>
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166 <expand macro="pluspf_08gb"/>
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167 <expand macro="pluspf_16gb"/>
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168 <expand macro="pluspfp_08gb"/>
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169 <expand macro="pluspfp_16gb"/>
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170 </param>
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171 </when>
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172 </conditional>
5
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
iuc
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173 </when>
0
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174 <when value="minikraken">
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175 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
1
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176 <option value="v2">Version 2</option>
0
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177 <option value="v1">Version 1</option>
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178 </param>
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179 </when>
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180 <when value="special">
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181 <param name="special_database_type" type="select" multiple="false" label="Select database to build">
e4cdf82de430 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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182 <option value="greengenes">Greengenes</option>
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183 <option value="silva">Silva</option>
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184 <option value="rdp">RDP</option>
e4cdf82de430 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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185 </param>
e4cdf82de430 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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186 <expand macro="common_params" />
e4cdf82de430 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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187 </when>
e4cdf82de430 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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188 <when value="custom">
6
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189 <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" />
0
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190 <param name="custom_database_name" type="text" label="Name for this database" />
6
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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191 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
0
e4cdf82de430 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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192 <expand macro="common_params" />
e4cdf82de430 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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193 </when>
e4cdf82de430 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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194 </conditional>
e4cdf82de430 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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195 </inputs>
e4cdf82de430 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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196 <outputs>
e4cdf82de430 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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197 <data name="out_file" format="data_manager_json" />
e4cdf82de430 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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198 </outputs>
e4cdf82de430 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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199 <tests>
6
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200 <test expect_num_outputs="1">
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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201 <conditional name="database_type">
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202 <param name="database_type" value="custom" />
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203 <param name="custom_fasta" value="adapter.fa" />
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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204 <param name="custom_database_name" value="custom_database" />
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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205 <param name="skip_maps" value="true" />
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206 <param name="kmer_len" value="35" />
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207 <param name="minimizer_spaces" value="6"/>
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208 <param name="load_factor" value="0.7" />
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209 <param name="clean" truevalue="--clean"/>
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210 </conditional>
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211 <output name="out_file">
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212 <assert_contents>
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213 <has_text text="kraken2_databases"/>
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214 <has_text text="path"/>
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215 <has_text text="custom_database"/>
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216 </assert_contents>
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217 </output>
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218 </test>
0
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219 <test>
6
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220 <conditional name="database_type">
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221 <param name="database_type" value="standard_prebuilt" />
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222 <conditional name="prebuild">
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223 <param name="prebuilt_date" value="2022-06-07"/>
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224 <param name="prebuilt_db" value="standard_08gb"/>
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225 </conditional>
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226 </conditional>
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227 <output name="out_file">
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228 <assert_contents>
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229 <has_text text="kraken2_databases"/>
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230 <has_text text="path"/>
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231 <has_text text="Standard-8"/>
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232 <has_text text="_standard_prebuilt_standard_08gb_2022-06-07"/>
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233 <has_text text="Version"/>
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234 <has_text text="Downloaded"/>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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235 </assert_contents>
9002633b4737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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236 </output>
0
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237 </test>
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238 </tests>
6
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239 <help><![CDATA[
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240 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
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241 ]]></help>
0
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242 <citations>
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243 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
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244 </citations>
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245 </tool>