Mercurial > repos > devteam > data_manager_build_kraken_database
annotate data_manager/kraken_database_builder.xml @ 4:1de1817a8a57 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit ae0b6f9da114f0889a8d31411d2f2c9bbf0c2004
| author | devteam |
|---|---|
| date | Tue, 14 Jun 2016 15:52:00 -0400 |
| parents | 404ba485ec01 |
| children | 6f0294046f41 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
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4
1de1817a8a57
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit ae0b6f9da114f0889a8d31411d2f2c9bbf0c2004
devteam
parents:
3
diff
changeset
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2 <tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.1"> |
| 0 | 3 <description>database builder</description> |
| 4 <requirements> | |
|
4
1de1817a8a57
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/data_managers/data_manager_build_kraken_database/ commit ae0b6f9da114f0889a8d31411d2f2c9bbf0c2004
devteam
parents:
3
diff
changeset
|
5 <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement> |
| 0 | 6 <requirement type="package" version="1.1.11">jellyfish</requirement> |
| 7 <requirement type="set_environment">KRAKEN_SCRIPT_PATH</requirement> | |
| 8 </requirements> | |
| 9 <stdio> | |
| 10 <exit_code description="Error" level="fatal" range="1:" /> | |
| 11 </stdio> | |
| 12 <version_command>kraken -version | awk '{print $NF}'</version_command> | |
| 13 <command> | |
| 14 <![CDATA[ | |
| 15 #set $library_list = str($libraries).split(',') | |
| 16 mkdir kraken-database && cd kraken-database && | |
| 17 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" && | |
| 18 #for $library in $library_list: | |
| 2 | 19 #if str($library) != 'None': |
| 20 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}" && | |
| 21 #end if | |
| 0 | 22 #end for |
| 23 #for $fasta in $input_fasta: | |
| 3 | 24 #if str($fasta) != 'None': |
| 25 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" && | |
| 26 #end if | |
| 0 | 27 #end for |
| 28 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && | |
| 29 cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}" | |
| 30 ]]> | |
| 31 </command> | |
| 32 <inputs> | |
| 33 <param label="Name for this database" name="database_name" type="text" /> | |
| 34 <param label="Select partial library to download" multiple="True" name="libraries" type="select"> | |
| 35 <option value="bacteria">Bacteria</option> | |
| 36 <option value="plasmids">Plasmids</option> | |
| 37 <option value="viruses">Viruses</option> | |
| 38 <option value="human">Human</option> | |
| 39 </param> | |
| 1 | 40 <param format="fasta" label="Select history item" multiple="True" name="input_fasta" optional="True" type="data" /> |
| 0 | 41 <param label="K-mer length in BP" name="kmer_len" type="integer" value="31" /> |
| 42 <param label="Minimizer length" name="minimizer_len" type="integer" value="15" /> | |
| 43 </inputs> | |
| 44 <outputs> | |
| 45 <data format="data_manager_json" name="out_file" /> | |
| 46 </outputs> | |
| 47 <citations> | |
| 48 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> | |
| 49 </citations> | |
| 3 | 50 </tool> |