Mercurial > repos > dfornika > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.xml @ 19:ffeb852407d6 draft default tip

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"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 6f21145d4103d33c227f52dc55a7d3dcf52f4f5d-dirty"
author dfornika
date Wed, 23 Oct 2019 14:21:07 -0400
parents f005b6efd096
children
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17
4c9f9d6098eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
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1 <?xml version="1.0"?>
19
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2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta_galaxy1">
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3 <macros>
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4 <xml name="common_params">
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5 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
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6 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
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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>
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10 </macros>
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11 <description>database builder</description>
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12 <requirements>
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13 <requirement type="package" version="2.0.8_beta">kraken2</requirement>
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14 </requirements>
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15 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
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16 <command detect_errors="exit_code">
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17 <![CDATA[
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18 python '$__tool_directory__/kraken2_build_database.py'
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19 '${out_file}'
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20 --database-type ${database_type.database_type}
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21 #if $database_type.database_type == "minikraken"
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22 --minikraken2-version ${database_type.minikraken2_version}
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23 #else if $database_type.database_type == "standard"
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24 --threads \${GALAXY_SLOTS:-1}
4c9f9d6098eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
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25 --kmer-len ${database_type.kmer_len}
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26 --minimizer-len ${database_type.minimizer_len}
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27 --minimizer-spaces ${database_type.minimizer_spaces}
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28 ${database_type.clean}
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29 #else if $database_type.database_type == "special"
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30 --threads \${GALAXY_SLOTS:-1}
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31 --special-database-type ${database_type.special_database_type}
4c9f9d6098eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
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32 --kmer-len ${database_type.kmer_len}
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33 --minimizer-len ${database_type.minimizer_len}
4c9f9d6098eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
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34 --minimizer-spaces ${database_type.minimizer_spaces}
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35 ${database_type.clean}
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36 #else if $database_type.database_type == "custom"
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37 --threads \${GALAXY_SLOTS:-1}
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38 ${database_type.skip_maps}
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39 --custom-fasta ${database_type.custom_fasta}
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40 --custom-database-name ${database_type.custom_database_name}
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41 --kmer-len ${database_type.kmer_len}
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42 --minimizer-len ${database_type.minimizer_len}
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43 --minimizer-spaces ${database_type.minimizer_spaces}
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44 ${database_type.clean}
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45 #end if
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46 ]]>
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47 </command>
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48 <inputs>
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49 <conditional name="database_type">
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50 <param name="database_type" type="select" multiple="false" label="Database Type">
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51 <option value="standard">Standard</option>
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52 <option value="minikraken">MiniKraken</option>
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53 <option value="special">Special</option>
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54 <option value="custom">Custom</option>
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55 </param>
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56 <when value="standard">
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57 <expand macro="common_params" />
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58 </when>
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59 <when value="minikraken">
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60 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
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61 <option value="v2">Version 2</option>
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62 <option value="v1">Version 1</option>
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63 </param>
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64 </when>
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65 <when value="special">
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66 <param name="special_database_type" type="select" multiple="false" label="Select database to build">
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67 <option value="greengenes">Greengenes</option>
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68 <option value="silva">Silva</option>
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69 <option value="rdp">RDP</option>
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70 </param>
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71 <expand macro="common_params" />
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72 </when>
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73 <when value="custom">
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74 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
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75 <param name="custom_database_name" type="text" label="Name for this database" />
18
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76 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
17
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77 <expand macro="common_params" />
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78 </when>
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79 </conditional>
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80 </inputs>
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81 <outputs>
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82 <data name="out_file" format="data_manager_json" />
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83 </outputs>
18
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84 <tests>
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85 <test>
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86 <param name="database_type" value="custom" />
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87 <param name="custom_fasta" value="adapter.fa" />
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88 <param name="custom_database_name" value="database" />
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89 <param name="skip_maps" value="true" />
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90 <output name="out_file" value="kraken2_custom_data_manager.json" />
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91 </test>
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92 </tests>
17
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93 <help>
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94 </help>
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95 <citations>
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96 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
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97 </citations>
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98 </tool>