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comparison data_manager/kraken_database_builder.xml @ 5:6f0294046f41 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken_database/ commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 17:49:05 -0400
parents 1de1817a8a57
children 4e6e90f31ffe
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4:1de1817a8a57 5:6f0294046f41
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.1"> 2 <tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.2">
3 <description>database builder</description> 3 <description>database builder</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement> 5 <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement>
6 <requirement type="package" version="1.1.11">jellyfish</requirement>
7 <requirement type="set_environment">KRAKEN_SCRIPT_PATH</requirement>
8 </requirements> 6 </requirements>
9 <stdio>
10 <exit_code description="Error" level="fatal" range="1:" />
11 </stdio>
12 <version_command>kraken -version | awk '{print $NF}'</version_command> 7 <version_command>kraken -version | awk '{print $NF}'</version_command>
13 <command> 8 <command detect_errors="exit_code">
14 <![CDATA[ 9 <![CDATA[
15 #set $library_list = str($libraries).split(',') 10 #set $library_list = str($libraries).split(',')
16 mkdir kraken-database && cd kraken-database && 11 mkdir kraken-database && cd kraken-database &&
17 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" && 12 kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' &&
18 #for $library in $library_list: 13 #for $library in $library_list:
19 #if str($library) != 'None': 14 #if str($library) != 'None':
20 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}" && 15 kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' &&
21 #end if 16 #end if
22 #end for 17 #end for
23 #for $fasta in $input_fasta: 18 #for $fasta in $input_fasta:
24 #if str($fasta) != 'None': 19 #if str($fasta) != 'None':
25 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" && 20 kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' &&
26 #end if 21 #end if
27 #end for 22 #end for
28 kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && 23 kraken-build --threads \${GALAXY_SLOTS:-1} --db '${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 "${out_file}" 24 cd .. &&
25 python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
30 ]]> 26 ]]>
31 </command> 27 </command>
32 <inputs> 28 <inputs>
33 <param label="Name for this database" name="database_name" type="text" /> 29 <param name="database_name" type="text" label="Name for this database" />
34 <param label="Select partial library to download" multiple="True" name="libraries" type="select"> 30 <param name="libraries" type="select" multiple="true" label="Select partial library to download">
35 <option value="bacteria">Bacteria</option> 31 <option value="bacteria">Bacteria</option>
36 <option value="plasmids">Plasmids</option> 32 <option value="plasmids">Plasmids</option>
37 <option value="viruses">Viruses</option> 33 <option value="viruses">Viruses</option>
38 <option value="human">Human</option> 34 <option value="human">Human</option>
39 </param> 35 </param>
40 <param format="fasta" label="Select history item" multiple="True" name="input_fasta" optional="True" type="data" /> 36 <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
41 <param label="K-mer length in BP" name="kmer_len" type="integer" value="31" /> 37 <param name="kmer_len" type="integer" value="31" label="K-mer length in BP" />
42 <param label="Minimizer length" name="minimizer_len" type="integer" value="15" /> 38 <param name="minimizer_len" type="integer" value="15" label="Minimizer length" />
43 </inputs> 39 </inputs>
44 <outputs> 40 <outputs>
45 <data format="data_manager_json" name="out_file" /> 41 <data name="out_file" format="data_manager_json" />
46 </outputs> 42 </outputs>
43 <help>
44 </help>
47 <citations> 45 <citations>
48 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> 46 <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
49 </citations> 47 </citations>
50 </tool> 48 </tool>