Mercurial > repos > iuc > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.xml @ 2:edacc4bcd3cb 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 1c0a28222ac235e77b2a792c1ebca027a746c220"
author iuc
date Sun, 22 Dec 2019 11:57:46 -0500
parents 6ba1ec5f86fc
children 0eebe086fd58
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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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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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2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta+galaxy2" profile="18.09">
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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>
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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4 <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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5 <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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6 <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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7 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
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8 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
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9 </xml>
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 </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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11 <description>database builder</description>
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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12 <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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13 <requirement type="package" version="2.0.8_beta">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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14 <requirement type="package" version="3.7">python</requirement>
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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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15 </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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16 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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17 <command detect_errors="exit_code">
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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18 <![CDATA[
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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19 python '$__tool_directory__/kraken2_build_database.py'
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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20 '${out_file}'
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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21 --database-type ${database_type.database_type}
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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22 #if $database_type.database_type == "minikraken"
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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23 --minikraken2-version ${database_type.minikraken2_version}
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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24 #else if $database_type.database_type == "standard"
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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25 --threads \${GALAXY_SLOTS:-1}
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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26 --kmer-len ${database_type.kmer_len}
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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27 --minimizer-len ${database_type.minimizer_len}
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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28 --minimizer-spaces ${database_type.minimizer_spaces}
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29 ${database_type.clean}
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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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30 #else if $database_type.database_type == "special"
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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31 --threads \${GALAXY_SLOTS:-1}
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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32 --special-database-type ${database_type.special_database_type}
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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33 --kmer-len ${database_type.kmer_len}
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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34 --minimizer-len ${database_type.minimizer_len}
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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35 --minimizer-spaces ${database_type.minimizer_spaces}
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36 ${database_type.clean}
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37 #else if $database_type.database_type == "custom"
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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38 --threads \${GALAXY_SLOTS:-1}
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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39 ${database_type.skip_maps}
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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40 --custom-fasta ${database_type.custom_fasta}
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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41 --custom-database-name ${database_type.custom_database_name}
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42 --kmer-len ${database_type.kmer_len}
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43 --minimizer-len ${database_type.minimizer_len}
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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44 --minimizer-spaces ${database_type.minimizer_spaces}
1
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45 ${database_type.clean}
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46 #end if
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47 ]]>
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48 </command>
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49 <inputs>
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50 <conditional name="database_type">
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51 <param name="database_type" type="select" multiple="false" label="Database Type">
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52 <option value="standard">Standard</option>
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53 <option value="minikraken">MiniKraken</option>
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54 <option value="special">Special</option>
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55 <option value="custom">Custom</option>
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56 </param>
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57 <when value="standard">
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58 <expand macro="common_params" />
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59 </when>
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60 <when value="minikraken">
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61 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
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62 <option value="v2">Version 2</option>
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63 <option value="v1">Version 1</option>
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64 </param>
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65 </when>
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66 <when value="special">
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67 <param name="special_database_type" type="select" multiple="false" label="Select database to build">
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68 <option value="greengenes">Greengenes</option>
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69 <option value="silva">Silva</option>
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70 <option value="rdp">RDP</option>
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71 </param>
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72 <expand macro="common_params" />
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73 </when>
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74 <when value="custom">
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75 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
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76 <param name="custom_database_name" type="text" label="Name for this database" />
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77 <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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78 <expand macro="common_params" />
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79 </when>
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80 </conditional>
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81 </inputs>
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82 <outputs>
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83 <data name="out_file" format="data_manager_json" />
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="database_type" value="custom" />
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88 <param name="custom_fasta" value="adapter.fa" />
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89 <param name="custom_database_name" value="database" />
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90 <param name="skip_maps" value="true" />
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91 <output name="out_file" value="kraken2_custom_data_manager.json" />
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92 </test>
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93 </tests>
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94 <help>
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95 </help>
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96 <citations>
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97 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
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98 </citations>
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99 </tool>