Mercurial > repos > dave > data_manager_build_kraken2_database
annotate data_manager/kraken2_build_database.xml @ 0:bd47b9f87d67 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
author | dave |
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date | Tue, 01 Dec 2020 16:07:40 +0000 |
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bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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1 <?xml version="1.0"?> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0" profile="18.09"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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3 <macros> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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4 <token name="@TOOL_VERSION@">2.1.1</token> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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5 <xml name="common_params"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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6 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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7 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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8 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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9 <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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10 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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11 </xml> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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12 </macros> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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13 <description>database builder</description> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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14 <requirements> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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15 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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16 <requirement type="package" version="3.7">python</requirement> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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17 </requirements> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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18 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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19 <command detect_errors="exit_code"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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20 <![CDATA[ |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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21 python '$__tool_directory__/kraken2_build_database.py' |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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22 '${out_file}' |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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23 --database-type ${database_type.database_type} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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24 #if $database_type.database_type == "minikraken" |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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25 --minikraken2-release $database_type.kraken_release |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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26 #if $database_type.kraken_release == "April_2019": |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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27 --minikraken2-version ${database_type.kraken_release.minikraken2_version} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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28 #end if |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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29 #else if $database_type.database_type == "standard" |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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30 --threads \${GALAXY_SLOTS:-1} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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31 --kmer-len ${database_type.kmer_len} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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32 --minimizer-len ${database_type.minimizer_len} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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33 --minimizer-spaces ${database_type.minimizer_spaces} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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34 --load-factor ${database_type.load_factor} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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35 ${database_type.clean} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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36 #else if $database_type.database_type == "special" |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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37 --threads \${GALAXY_SLOTS:-1} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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38 --special-database-type ${database_type.special_database_type} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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39 --kmer-len ${database_type.kmer_len} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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40 --minimizer-len ${database_type.minimizer_len} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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41 --minimizer-spaces ${database_type.minimizer_spaces} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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42 --load-factor ${database_type.load_factor} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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43 ${database_type.clean} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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44 #else if $database_type.database_type == "custom" |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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45 --threads \${GALAXY_SLOTS:-1} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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46 ${database_type.skip_maps} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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47 --custom-fasta ${database_type.custom_fasta} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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48 --custom-database-name ${database_type.custom_database_name} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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49 --kmer-len ${database_type.kmer_len} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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50 --minimizer-len ${database_type.minimizer_len} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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51 --minimizer-spaces ${database_type.minimizer_spaces} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
parents:
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52 --load-factor ${database_type.load_factor} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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53 ${database_type.clean} |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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54 #end if |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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55 ]]> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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56 </command> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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57 <inputs> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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58 <conditional name="database_type"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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59 <param name="database_type" type="select" multiple="false" label="Database Type"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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60 <option value="standard">Standard</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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61 <option value="minikraken">MiniKraken</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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62 <option value="special">Special</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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63 <option value="custom">Custom</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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64 </param> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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65 <when value="standard"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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66 <expand macro="common_params" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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67 </when> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
dave
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68 <when value="minikraken"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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69 <conditional name="kraken_release"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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70 <param name="minikraken2_release" type="select" multiple="false" label="Select the MiniKraken2 release to download"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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71 <option value="April_2019">April 2019</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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72 <option value="March_2020">March 2020</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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73 </param> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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74 <when value="April_2019"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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75 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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76 <option value="v2">Version 2</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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77 <option value="v1">Version 1</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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78 </param> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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79 </when> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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80 <when value="March_2020" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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81 </conditional> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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82 </when> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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83 <when value="special"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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84 <param name="special_database_type" type="select" multiple="false" label="Select database to build"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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85 <option value="greengenes">Greengenes</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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86 <option value="silva">Silva</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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87 <option value="rdp">RDP</option> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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88 </param> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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89 <expand macro="common_params" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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90 </when> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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91 <when value="custom"> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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92 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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93 <param name="custom_database_name" type="text" label="Name for this database" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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94 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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95 <expand macro="common_params" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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96 </when> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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97 </conditional> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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98 </inputs> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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99 <outputs> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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100 <data name="out_file" format="data_manager_json" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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101 </outputs> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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102 <tests> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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103 <test> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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104 <param name="database_type" value="custom" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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105 <param name="custom_fasta" value="adapter.fa" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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106 <param name="custom_database_name" value="database" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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107 <param name="skip_maps" value="true" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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108 <output name="out_file" value="kraken2_custom_data_manager.json" /> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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109 </test> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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110 </tests> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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111 <help> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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112 </help> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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113 <citations> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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114 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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115 </citations> |
bd47b9f87d67
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff-dirty"
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116 </tool> |