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1 <?xml version="1.0"?>
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2 <tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.0">
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3 <description>database builder</description>
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4 <requirements>
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5 <requirement type="package" version="0.10.5">kraken</requirement>
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6 <requirement type="package" version="1.1.11">jellyfish</requirement>
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7 <requirement type="set_environment">KRAKEN_SCRIPT_PATH</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code description="Error" level="fatal" range="1:" />
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11 </stdio>
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12 <version_command>kraken -version | awk '{print $NF}'</version_command>
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13 <command>
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14 <![CDATA[
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15 #set $library_list = str($libraries).split(',')
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16 mkdir kraken-database && cd kraken-database &&
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17 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" &&
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18 #for $library in $library_list:
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2
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19 #if str($library) != 'None':
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20 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}" &&
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21 #end if
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22 #end for
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23 #for $fasta in $input_fasta:
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24 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" &&
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25 #end for
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26 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} &&
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27 cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}"
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28 ]]>
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29 </command>
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30 <inputs>
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31 <param label="Name for this database" name="database_name" type="text" />
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32 <param label="Select partial library to download" multiple="True" name="libraries" type="select">
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33 <option value="bacteria">Bacteria</option>
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34 <option value="plasmids">Plasmids</option>
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35 <option value="viruses">Viruses</option>
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36 <option value="human">Human</option>
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37 </param>
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38 <param format="fasta" label="Select history item" multiple="True" name="input_fasta" optional="True" type="data" />
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39 <param label="K-mer length in BP" name="kmer_len" type="integer" value="31" />
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40 <param label="Minimizer length" name="minimizer_len" type="integer" value="15" />
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41 </inputs>
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42 <outputs>
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43 <data format="data_manager_json" name="out_file" />
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44 </outputs>
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45 <citations>
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46 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
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47 </citations>
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48 </tool> |
