Mercurial > repos > devteam > data_manager_build_kraken_database
changeset 5:6f0294046f41 draft
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 |
| files | data_manager/kraken_database_builder.xml data_manager/make_json.py tool_dependencies.xml |
| diffstat | 3 files changed, 22 insertions(+), 37 deletions(-) [+] |
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--- a/data_manager/kraken_database_builder.xml Tue Jun 14 15:52:00 2016 -0400 +++ b/data_manager/kraken_database_builder.xml Tue Apr 04 17:49:05 2017 -0400 @@ -1,49 +1,47 @@ <?xml version="1.0"?> -<tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.1"> +<tool id="kraken_database_builder" name="Kraken" tool_type="manage_data" version="1.0.2"> <description>database builder</description> <requirements> <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement> - <requirement type="package" version="1.1.11">jellyfish</requirement> - <requirement type="set_environment">KRAKEN_SCRIPT_PATH</requirement> </requirements> - <stdio> - <exit_code description="Error" level="fatal" range="1:" /> - </stdio> <version_command>kraken -version | awk '{print $NF}'</version_command> - <command> + <command detect_errors="exit_code"> <![CDATA[ #set $library_list = str($libraries).split(',') mkdir kraken-database && cd kraken-database && - kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db "${database_name}" && + kraken-build --threads \${GALAXY_SLOTS:-1} --download-taxonomy --db '${database_name}' && #for $library in $library_list: #if str($library) != 'None': - kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db "${database_name}" && + kraken-build --threads \${GALAXY_SLOTS:-1} --download-library $library --db '${database_name}' && #end if #end for #for $fasta in $input_fasta: #if str($fasta) != 'None': - kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --add-to-library "$fasta" && + kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --add-to-library '$fasta' && #end if #end for - kraken-build --threads \${GALAXY_SLOTS:-1} --db "${database_name}" --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && - cd .. && python \$KRAKEN_SCRIPT_PATH/data_manager/make_json.py --db "${database_name}" --out "${out_file}" + kraken-build --threads \${GALAXY_SLOTS:-1} --db '${database_name}' --build --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} && + cd .. && + python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}' ]]> </command> <inputs> - <param label="Name for this database" name="database_name" type="text" /> - <param label="Select partial library to download" multiple="True" name="libraries" type="select"> + <param name="database_name" type="text" label="Name for this database" /> + <param name="libraries" type="select" multiple="true" label="Select partial library to download"> <option value="bacteria">Bacteria</option> <option value="plasmids">Plasmids</option> <option value="viruses">Viruses</option> <option value="human">Human</option> </param> - <param format="fasta" label="Select history item" multiple="True" name="input_fasta" optional="True" type="data" /> - <param label="K-mer length in BP" name="kmer_len" type="integer" value="31" /> - <param label="Minimizer length" name="minimizer_len" type="integer" value="15" /> + <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" /> + <param name="kmer_len" type="integer" value="31" label="K-mer length in BP" /> + <param name="minimizer_len" type="integer" value="15" label="Minimizer length" /> </inputs> <outputs> - <data format="data_manager_json" name="out_file" /> + <data name="out_file" format="data_manager_json" /> </outputs> + <help> + </help> <citations> <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations>
--- a/data_manager/make_json.py Tue Jun 14 15:52:00 2016 -0400 +++ b/data_manager/make_json.py Tue Apr 04 17:49:05 2017 -0400 @@ -1,13 +1,8 @@ +import argparse import json -import argparse import os import shutil -parser = argparse.ArgumentParser(description='Create data manager json.') -parser.add_argument('--db', dest='database', action='store', help='Database name') -parser.add_argument('--out', dest='output', action='store', help='JSON filename') - -args = parser.parse_args() def main(args): data_manager_entry = {} @@ -23,6 +18,10 @@ shutil.move(os.path.join(output_path, filename), target_directory) file(args.output, 'w').write(json.dumps(data_manager_json)) + if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Create data manager json.') + parser.add_argument('--db', dest='database', action='store', help='Database name') + parser.add_argument('--out', dest='output', action='store', help='JSON filename') + args = parser.parse_args() main(args) -
--- a/tool_dependencies.xml Tue Jun 14 15:52:00 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <set_environment version="1.0"> - <environment_variable action="set_to" name="KRAKEN_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> - <package name="kraken" version="0.10.6-eaf8fb68"> - <repository changeset_revision="6dc210626044" name="package_kraken_0_10_6_eaf8fb68" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="jellyfish" version="1.1.11"> - <repository changeset_revision="9529f5e46f4e" name="package_jellyfish_1_1_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>