Mercurial > repos > iuc > data_manager_build_bracken_database

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
author iuc
date Wed, 05 Nov 2025 13:31:43 +0000
parents cef566388a0f
children
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cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
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1 <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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2 <description>bracken database builder</description>
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cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
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3 <macros>
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a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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4 <token name="@TOOL_VERSION@">3.1</token>
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cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
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5 <token name="@VERSION_SUFFIX@">0</token>
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a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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6 <token name="@PROFILE@">24.0</token>
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cef566388a0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit db62b99fe2c0e77e7ee63da5fb315f4b6d95170b
iuc
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7 </macros>
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0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">bracken</requirement>
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0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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10 </requirements>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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11 <command>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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12 <![CDATA[
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a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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13 #set $db_dir = $out_file.extra_files_path
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14 mkdir '$db_dir' &&
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a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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16 ## Create symlinks to the contents of the kraken database, since otherwise
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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17 ## the DM tool (ie bracken-build) would write to the kraken DB folder.
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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18 ##
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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19 ## These symlinks will be part of the final db_dir which will be moved
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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20 ## to the tool-data (except for some of the pre-exsting *mers.kraken
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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21 ## and *mers.kmer_distrib which may be deleted -- depending on the
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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22 ## choice of prebuilt).
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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23 ## Hence the final db_dir will have
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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24 ## - either a created mers.kmer_distrib file or a symlink pointing to the kraken2 db source
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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25 ## - either a created mers.kraken file or a symlink pointing to the kraken2 db source
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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26 ## - and symlinks to the krakenDB
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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27 ## Note that in the data table entry only the path to mers.kmer_distrib file is used
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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28 ln -s '${kraken_db.fields.path}'/* '$db_dir/' &&
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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30 #if $check_prebuilt.prebuilt == "no"
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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31 ## remove any other pre-existing bracken-build results
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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32 find '$db_dir' -maxdepth 1 -name "*mers*" -delete &&
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
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33 bracken-build
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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34 -t "\${GALAXY_SLOTS:-1}"
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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35 -k $check_prebuilt.kmer_len
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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36 -l $check_prebuilt.read_len
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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37 -d '$db_dir/'
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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38 #else
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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39 if [ ! -e '$db_dir/database${check_prebuilt.read_len}mers.kmer_distrib' ]; then
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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40 >&2 echo "Have you chosen the correct k-mer length? file $db_dir/database${check_prebuilt.read_len}mers.kmer_distrib does not exist.";
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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41 exit 1;
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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42 fi
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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43 ## delete any other (links to) prebuilt bracken databases (except the one of the chosen read_len)
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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44 && find '$db_dir' -maxdepth 1 -name "*mers.kraken" -a \! -name "*${check_prebuilt.read_len}mers.kraken" -delete
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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45 && find '$db_dir' -maxdepth 1 -name "*mers.kmer_distrib" -a \! -name "*${check_prebuilt.read_len}mers.kmer_distrib" -delete
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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46 #end if
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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47 && cp '$dmjson' '$out_file'
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0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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48 ]]>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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49 </command>
6
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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50 <configfiles>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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51 <configfile name="dmjson"><![CDATA[#slurp
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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52 #import uuid
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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53 #set $database_value = str(uuid.uuid4())
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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54 #set $db_dir = $out_file.extra_files_path
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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55
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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56 #if $database_name == ""
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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57 #if $check_prebuilt.prebuilt == "no"
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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58 #set $database_name = $kraken_db.fields.name + " (k-mer length = " + str($check_prebuilt.kmer_len) +", read length = " + str($check_prebuilt.read_len) + ")"
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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59 #else
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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60 #set $database_name = $kraken_db.fields.name + " (Prebuilt bracken DB with read length = " + str($check_prebuilt.read_len) + ")"
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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61 #end if
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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62 #end if
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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63 {
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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64 "data_tables":{
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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65 "bracken_databases":[
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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66 {
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67 "value": "$database_value",
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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68 "name": "$database_name",
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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69 "path": "$db_dir/database${check_prebuilt.read_len}mers.kmer_distrib"
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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70 }
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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71 ]
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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72 }
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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73 }]]></configfile>
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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74 </configfiles>
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0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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75 <inputs>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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76 <param name="kraken_db" type="select">
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77 <options from_data_table="kraken2_databases">
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78 <validator type="no_options" message="No Kraken2 databases are available" />
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79 </options>
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80 </param>
3
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81 <conditional name="check_prebuilt">
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82 <param name="prebuilt" type="select" label="Use Pre-built DB" help="Use existing pre-built DB. This only works for kraken DBs, that already contain additional bracken DBs. This is the case for DBs downloaded from https://benlangmead.github.io/aws-indexes/k2.">
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83 <option value="no">No</option>
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84 <option value="yes">Yes</option>
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85 </param>
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86 <when value="no">
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87 <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" help="The K-mer length of the bracken DB should be identical to the K-mer length used to build the kraken2 DB." />
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88 <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" help="The read length of the bracken DB should be the same as the length of the reads to be analysis (one read in case of paired reads)." />
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89 </when>
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90 <when value="yes">
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91 <param name="read_len" type="select" label="Read length" help="The read length of the bracken DB should be the same as the length of the reads to be analysis (one read in case of paired reads). The prebuilt DBs where built using the same K-mer length as the kraken2 DB.">
3
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92 <option value="50">50</option>
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93 <option value="75">75</option>
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94 <option value="100" selected="true">100</option>
3
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95 <option value="150">150</option>
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96 <option value="200">200</option>
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97 <option value="250">250</option>
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98 <option value="300">300</option>
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99 </param>
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100 </when>
6
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101 </conditional>
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102 <param name="database_name" type="text" label="Database Name" help="If left empty a name will be constructed from the name of the Kraken2 database suffixed by info on read and k-mer length. Otherwise please add a clear reference to the corresponding kraken2 DB the read length and kmer length to the name." />
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103 </inputs>
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104 <outputs>
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105 <data name="out_file" format="data_manager_json" />
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106 </outputs>
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107 <tests>
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108 <test>
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109 <param name="kraken_db" value="test_entry" />
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110 <param name="database_name" value="" />
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111 <conditional name="check_prebuilt">
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112 <param name="prebuilt" value="yes" />
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113 <param name="read_len" value="100" />
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114 </conditional>
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115 <output name="out_file">
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116 <assert_contents>
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117 <has_text text="Prebuilt bracken DB with read length = 100" />
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118 <has_text text="database100mers.kmer_distrib" />
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119 </assert_contents>
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120 </output>
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121 </test>
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122 <test>
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123 <param name="kraken_db" value="test_entry" />
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124 <param name="database_name" value="custom database name" />
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125 <conditional name="check_prebuilt">
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126 <param name="prebuilt" value="no" />
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127 <param name="read_len" value="150" />
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128 </conditional>
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129 <output name="out_file">
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130 <assert_contents>
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131 <has_text text="custom database name" />
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132 <has_text text="database150mers.kmer_distrib" />
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133 </assert_contents>
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134 </output>
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135 </test>
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136 </tests>
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137 <help>
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138 A bracken DB can only be built as an addition to an existing kracken2 DB (see `Bracken docs`_).
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139
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140 .. _Bracken docs: https://github.com/jenniferlu717/Bracken?tab=readme-ov-file#step-1-generate-the-bracken-database-file-databasexmerskmer_distrib-1
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141
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142 ======================================
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143 Using prebuilt DBs
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144 ======================================
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145
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146 The prebuilt option does use existing bracken DBs, that are shipped with kraken2 DBs. This is the case for DBs downloaded from https://benlangmead.github.io/aws-indexes/k2.
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147 All prebuilt databases contain a Kraken 2 database along with Bracken databases built for 50, 75, 100, 150, 200, 250 and 300 read lengths (referring to the length of the sequenced reads to be analysis using that database (one read in case of paired reads)).
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148 In this case the data manager points to the same DB as the kracken2 DB.
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149 Note the Kraken 2 / Bracken 16s DBs only contain the Bracken databases built for 100mers, 150mers, and 200mers.
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150 **The prebuilt option must not be used for custom kraken2 DBs ! For this the bracken DB needs to be build.**
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151
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152 ======================================
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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153 Building new DBs
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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154 ======================================
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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155
a0f18c07696a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_bracken_database commit a108f20aebc04574a8bd0a90b955064439a50852
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156 Use the same K-mer length as the kraken2 DB and choose read lengths that are close to the read length of the analysis you want to perform (one read in case of paired reads).
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0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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157 </help>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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158 <citations>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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159 <citation type="doi">10.7717/peerj-cs.104</citation>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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160 </citations>
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
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161 </tool>