annotate data_manager/kraken2_build_database.xml @ 0:c13785ca6192 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
author nate
date Wed, 06 Nov 2024 20:00:39 +0000
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c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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1 <?xml version="1.0"?>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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3 <description>database builder</description>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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4 <macros>
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5 <token name="@TOOL_VERSION@">2.1.3</token>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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6 <token name="@VERSION_SUFFIX@">3</token>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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7 <token name="@PROFILE@">22.01</token>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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8 <xml name="common_params">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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9 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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10 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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11 <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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12 <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" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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13 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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14 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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15 <xml name="viral">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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16 <option value="viral">Viral (viral; ~0.5 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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17 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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18 <xml name="minusb">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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19 <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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20 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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21 <xml name="standard">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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22 <option value="standard">Standard-Full (archaea, bacteria, viral, plasmid, human, UniVec_Core; ~50 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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23 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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24 <xml name="standard_08gb">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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25 <option value="standard_08gb">Standard-8 (Standard with DB capped at 8 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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26 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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27 <xml name="standard_16gb">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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28 <option value="standard_16gb">Standard-16 (Standard with DB capped at 16 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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29 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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30 <xml name="pluspf">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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31 <option value="pluspf">PlusPF (Standard plus protozoa and fungi; ~50 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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32 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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33 <xml name="pluspf_08gb">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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34 <option value="pluspf_08gb">PlusPF-8 (PlusPF with DB capped at 8 GB; ~7.5 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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35 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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36 <xml name="pluspf_16gb">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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37 <option value="pluspf_16gb">PlusPF-16 (PlusPF with DB capped at 16 GB; ~15 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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38 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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39 <xml name="pluspfp">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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40 <option value="pluspfp">PlusPFP (Standard plus protozoa, fungi and plant; ~129 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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41 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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42 <xml name="pluspfp_08gb">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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43 <option value="pluspfp_08gb">PlusPFP-8 (PlusPFP with DB capped at 8 GB; ~7.5 GB)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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44 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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45 <xml name="pluspfp_16gb">
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46 <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
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47 </xml>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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48 </macros>
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49 <xrefs>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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50 <xref type="bio.tools">kraken2</xref>
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51 </xrefs>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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52 <requirements>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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53 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
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54 <requirement type="package" version="3.13">python</requirement>
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55 </requirements>
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56 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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57 <command detect_errors="exit_code"><![CDATA[
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58 python '$__tool_directory__/kraken2_build_database.py'
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59 '$out_file'
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60 --database-type '$database_type.database_type'
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61 #if $database_type.database_type == "standard_local_build"
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62 --threads \${GALAXY_SLOTS:-1}
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63 --kmer-len $database_type.kmer_len
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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64 --minimizer-len $database_type.minimizer_len
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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65 --minimizer-spaces $database_type.minimizer_spaces
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66 --load-factor $database_type.load_factor
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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67 $database_type.clean
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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68 #else if $database_type.database_type == "standard_prebuilt"
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69 --prebuilt-db '$database_type.prebuild.prebuilt_db'
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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70 --prebuilt-date '$database_type.prebuild.prebuilt_date'
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71 #else if $database_type.database_type == "minikraken"
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72 --minikraken2-version '$database_type.minikraken2_version'
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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73 #else if $database_type.database_type == "special_prebuilt"
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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74 --prebuilt-db '$database_type.special_prebuild.prebuilt_db'
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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75 --prebuilt-date '$database_type.special_prebuild.prebuilt_date'
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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76 #else if $database_type.database_type == "special"
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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77 --threads \${GALAXY_SLOTS:-1}
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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78 --special-database-type '$database_type.special_database_type'
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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79 --kmer-len $database_type.kmer_len
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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80 --minimizer-len $database_type.minimizer_len
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
81 --minimizer-spaces $database_type.minimizer_spaces
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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82 --load-factor $database_type.load_factor
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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83 $database_type.clean
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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84 #else if $database_type.database_type == "custom"
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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85 --threads \${GALAXY_SLOTS:-1}
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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86 --custom-fasta '$database_type.custom_fasta'
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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87 --custom-database-name '$database_type.custom_database_name'
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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88 --custom-source-info '$database_type.custom_source_info'
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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89 $database_type.skip_maps
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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90 --kmer-len $database_type.kmer_len
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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91 --minimizer-len $database_type.minimizer_len
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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92 --minimizer-spaces $database_type.minimizer_spaces
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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93 --load-factor $database_type.load_factor
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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94 $database_type.clean
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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95 #end if
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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96 ]]>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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97 </command>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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98 <inputs>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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99 <conditional name="database_type">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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100 <param name="database_type" type="select" multiple="false" label="Database Type">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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101 <option value="standard_local_build">Standard, Local Build</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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102 <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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103 <option value="minikraken">MiniKraken</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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104 <option value="special_prebuilt">Special Pre-Built indexes</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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105 <option value="special">Special</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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106 <option value="custom">Custom</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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107 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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108 <when value="standard_local_build">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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109 <expand macro="common_params" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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110 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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111 <when value="standard_prebuilt">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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112 <conditional name="prebuild">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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113 <param name="prebuilt_date" type="select" label="Select index build date">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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114 <option value="2024-06-05">June 5, 2024</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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115 <option value="2024-01-12">January 12, 2024</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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116 <option value="2023-06-05">June 5, 2023</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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117 <option value="2022-06-07">June 7, 2022</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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118 <option value="2021-05-17">May 17, 2021</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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119 <option value="2021-01-27">January 27, 2021</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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120 <option value="2020-12-02">December 2, 2020</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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121 <option value="2020-09-19">September 19, 2020</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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122 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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123 <when value="2024-06-05">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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124 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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125 <expand macro="viral"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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126 <expand macro="minusb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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127 <expand macro="standard"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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128 <expand macro="standard_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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129 <expand macro="standard_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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130 <expand macro="pluspf"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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131 <expand macro="pluspf_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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132 <expand macro="pluspf_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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133 <expand macro="pluspfp"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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134 <expand macro="pluspfp_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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135 <expand macro="pluspfp_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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136 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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137 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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138 <when value="2024-01-12">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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139 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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140 <expand macro="viral"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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141 <expand macro="minusb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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142 <expand macro="standard"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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143 <expand macro="standard_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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144 <expand macro="standard_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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145 <expand macro="pluspf"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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146 <expand macro="pluspf_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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147 <expand macro="pluspf_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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148 <expand macro="pluspfp"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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149 <expand macro="pluspfp_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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150 <expand macro="pluspfp_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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151 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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152 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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153 <when value="2023-06-05">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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154 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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155 <expand macro="viral"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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156 <expand macro="minusb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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157 <expand macro="standard"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
158 <expand macro="standard_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
159 <expand macro="standard_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
160 <expand macro="pluspf"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
161 <expand macro="pluspf_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
162 <expand macro="pluspf_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
163 <expand macro="pluspfp"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
164 <expand macro="pluspfp_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
165 <expand macro="pluspfp_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
166 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
167 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
168 <when value="2022-06-07">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
169 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
170 <expand macro="viral"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
171 <expand macro="minusb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
172 <expand macro="standard"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
173 <expand macro="standard_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
174 <expand macro="standard_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
175 <expand macro="pluspf"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
176 <expand macro="pluspf_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
177 <expand macro="pluspf_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
178 <expand macro="pluspfp"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
179 <expand macro="pluspfp_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
180 <expand macro="pluspfp_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
181 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
182 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
183 <when value="2021-05-17">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
184 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
185 <expand macro="viral"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
186 <expand macro="minusb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
187 <expand macro="standard"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
188 <expand macro="standard_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
189 <expand macro="standard_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
190 <expand macro="pluspf"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
191 <expand macro="pluspf_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
192 <expand macro="pluspf_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
193 <expand macro="pluspfp_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
194 <expand macro="pluspfp_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
195 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
196 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
197 <when value="2021-01-27">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
198 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
199 <expand macro="pluspf"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
200 <expand macro="pluspf_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
201 <expand macro="pluspf_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
202 <expand macro="pluspfp_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
203 <expand macro="pluspfp_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
204 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
205 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
206 <when value="2020-12-02">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
207 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
208 <expand macro="viral"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
209 <expand macro="minusb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
210 <expand macro="standard"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
211 <expand macro="standard_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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parents:
diff changeset
212 <expand macro="standard_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
213 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
214 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
215 <when value="2020-09-19">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
216 <param name="prebuilt_db" type="select" multiple="false" label="Select a prebuilt Refseq indexes to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
217 <expand macro="minusb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
218 <expand macro="standard"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
219 <expand macro="standard_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
220 <expand macro="standard_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
221 <expand macro="pluspf"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
222 <expand macro="pluspf_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
223 <expand macro="pluspf_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
224 <expand macro="pluspfp_08gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
225 <expand macro="pluspfp_16gb"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
226 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
227 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
228 </conditional>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
229 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
230 <when value="special_prebuilt">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
231 <conditional name="special_prebuild">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
232 <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
233 <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
234 <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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235 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
236 <when value="eupathdb48_20230407">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
237 <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
238 <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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diff changeset
239 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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240 <when value="eupathdb48_20201113">
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241 <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
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242 <param name="prebuilt_date" type="hidden" value="2020-11-13"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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243 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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244 </conditional>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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245 </when>
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246 <when value="minikraken">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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247 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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248 <option value="v2">Version 2</option>
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249 <option value="v1">Version 1</option>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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250 </param>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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251 </when>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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252 <when value="special">
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253 <param name="special_database_type" type="select" multiple="false" label="Select database to build">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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254 <option value="greengenes">Greengenes</option>
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255 <option value="silva">Silva</option>
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256 <option value="rdp">RDP</option>
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257 </param>
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258 <expand macro="common_params" />
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259 </when>
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260 <when value="custom">
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261 <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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262 <param name="custom_database_name" type="text" label="Name for this database" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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263 <param name="custom_source_info" type="text" label="Database source info" help="Concise description of how this build has been sourced. This description will be appended (in parentheses) to the user-facing name of the build. Example: https://doi.org/10.5281/zenodo.8339822, from v1 assembly_summary.txt sequences" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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264 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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265 <expand macro="common_params" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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266 </when>
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267 </conditional>
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268 </inputs>
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269 <outputs>
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270 <data name="out_file" format="data_manager_json" />
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271 </outputs>
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272 <tests>
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273 <test expect_num_outputs="1">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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274 <conditional name="database_type">
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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275 <param name="database_type" value="custom" />
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276 <param name="custom_fasta" value="adapter.fa" />
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277 <param name="custom_database_name" value="custom_database" />
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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278 <param name="custom_source_info" value="from adapter.fa test data" />
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279 <param name="skip_maps" value="true" />
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280 <param name="kmer_len" value="35" />
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281 <param name="minimizer_spaces" value="6"/>
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282 <param name="load_factor" value="0.7" />
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283 <param name="clean" value="true"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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284 </conditional>
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285 <output name="out_file">
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286 <assert_contents>
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287 <has_text text="kraken2_databases"/>
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288 <has_text text="path"/>
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289 <has_text text="custom_database (from adapter.fa test data, kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7)"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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290 </assert_contents>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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291 </output>
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292 </test>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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293 <test>
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294 <conditional name="database_type">
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295 <param name="database_type" value="standard_prebuilt" />
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296 <conditional name="prebuild">
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297 <param name="prebuilt_date" value="2022-06-07"/>
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298 <param name="prebuilt_db" value="viral"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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299 </conditional>
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300 </conditional>
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301 <output name="out_file">
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302 <assert_contents>
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303 <has_text text="kraken2_databases"/>
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304 <has_text text="path"/>
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305 <has_text text="Viral"/>
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306 <has_text text="_standard_prebuilt_viral_2022-06-07"/>
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307 <has_text text="Version"/>
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308 <has_text text="Downloaded"/>
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309 </assert_contents>
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310 </output>
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311 </test>
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312 <!-- test with latest version -->
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313 <test>
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314 <conditional name="database_type">
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315 <param name="database_type" value="standard_prebuilt" />
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316 <conditional name="prebuild">
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317 <param name="prebuilt_date" value="2024-01-12"/>
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318 <param name="prebuilt_db" value="viral"/>
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319 </conditional>
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320 </conditional>
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321 <output name="out_file">
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322 <assert_contents>
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323 <has_text text="kraken2_databases"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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324 <has_text text="path"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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325 <has_text text="Viral"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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326 <has_text text="_standard_prebuilt_viral_2024-01-12"/>
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327 <has_text text="Version"/>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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328 <has_text text="Downloaded"/>
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329 </assert_contents>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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330 </output>
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331 </test>
c13785ca6192 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
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332 <!-- test with first 2024 version -->
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333 <test>
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334 <conditional name="database_type">
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335 <param name="database_type" value="standard_prebuilt" />
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336 <conditional name="prebuild">
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337 <param name="prebuilt_date" value="2024-06-05"/>
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338 <param name="prebuilt_db" value="viral"/>
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339 </conditional>
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340 </conditional>
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341 <output name="out_file">
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342 <assert_contents>
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343 <has_text text="kraken2_databases"/>
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344 <has_text text="path"/>
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345 <has_text text="Viral"/>
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346 <has_text text="_standard_prebuilt_viral_2024-06-05"/>
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347 <has_text text="Version"/>
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348 <has_text text="Downloaded"/>
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349 </assert_contents>
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350 </output>
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351 </test>
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352 </tests>
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353 <help><![CDATA[
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354 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
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355 ]]></help>
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356 <citations>
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357 <citation type="doi">10.1186/s13059-019-1891-0</citation>
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358 </citations>
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359 </tool>