Mercurial > repos > estrain > data_manager_fastani
changeset 13:8897c156df99 draft
Uploaded
| author | estrain |
|---|---|
| date | Sun, 29 May 2022 21:44:36 +0000 |
| parents | dd5c2ac49386 |
| children | 0e06e944120b |
| files | data_manager_fastani/data_manager/data_manager_fastani.py data_manager_fastani/data_manager/data_manager_fastani.xml data_manager_fastani/data_manager_conf.xml |
| diffstat | 3 files changed, 14 insertions(+), 10 deletions(-) [+] |
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--- a/data_manager_fastani/data_manager/data_manager_fastani.py Sun May 29 20:51:41 2022 +0000 +++ b/data_manager_fastani/data_manager/data_manager_fastani.py Sun May 29 21:44:36 2022 +0000 @@ -11,7 +11,7 @@ import requests -def download_D1(output_directory): +def download_D1(output_directory,argsname): #FastANI databases from Kostas Lab url="http://enve-omics.ce.gatech.edu/data/public_fastani/D1.tar.gz" @@ -27,9 +27,12 @@ tarcmd="tar xvzf D1.tar.gz; rm -Rf D1.tar.gz" os.system(tarcmd) + cmd="mv D1 " + argsname + os.system(cmd) + os.chdir(cwd) - return output_directory + "/D1/" + return output_directory + "/" + argsname def download_VL(output_directory): @@ -76,7 +79,7 @@ parser = argparse.ArgumentParser(description='Download FastANI Databases') parser.add_argument('--type', type=str, required=True, nargs=1, help='Database Type') - parser.add_argument('--desc', type=str, required=True, nargs=1, help='Database Description') + parser.add_argument('--name', type=str, required=True, nargs=1, help='Unique Database Folder Name') parser.add_argument('--out', type=str, required=True, nargs=1, help='output file') args = parser.parse_args() @@ -90,13 +93,13 @@ #Fetch the files and build blast databases if(args.type[0]=="D1"): - output_directory=download_D1(output_directory) + output_directory=download_D1(output_directory,args.name[0]) version="FastANI D1" elif(args.type[0]=="VL"): - output_directory=download_D1(output_directory) + output_directory=download_D1(output_directory,args.name[0]) output_directory=download_VL(output_directory) version="FastANI D1 + VetLIRN" - print_json(version,output_directory,args.desc[0],args.out[0]) + print_json(version,output_directory,args.name[0],args.out[0]) if __name__ == "__main__": main()
--- a/data_manager_fastani/data_manager/data_manager_fastani.xml Sun May 29 20:51:41 2022 +0000 +++ b/data_manager_fastani/data_manager/data_manager_fastani.xml Sun May 29 21:44:36 2022 +0000 @@ -1,15 +1,16 @@ <tool id="data_manager_fastani" name="FastANI Data Manger" tool_type="manage_data" version="0.0.1" profile="20.01"> <requirements> + <requirement type="package">entrez-direct</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - python $__tool_directory__/data_manager_fastani.py --type $input_source_selector --desc $desc --out ${output_file}; + python $__tool_directory__/data_manager_fastani.py --type $input_source_selector --name $name --out ${output_file}; ]]></command> <inputs> <param name="input_source_selector" type="select" label="Database Selection"> <option value="D1">FastANI D1</option> <option value="VL">FastANI D1 + VetLIRN Fish Pathogens</option> </param> - <param name="desc" type="text" format="text" label="Database Name"/> + <param name="name" type="text" format="text" label="Database Name"/> </inputs> <outputs> <data name="output_file" format="data_manager_json"/>
--- a/data_manager_fastani/data_manager_conf.xml Sun May 29 20:51:41 2022 +0000 +++ b/data_manager_fastani/data_manager_conf.xml Sun May 29 21:44:36 2022 +0000 @@ -3,12 +3,12 @@ <data_manager tool_file="data_manager/data_manager_fastani.xml" id="data_manager_fastani"> <data_table name="fastani"> <output> + <column name="value" /> <column name="name" /> - <column name="description" /> <column name="path" output_ref="output_file" > <move type="directory" relativize_symlinks="True"> <src>${path}</src> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">fastani/${name}/</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">fastani/</target> </move> <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/fastani/${name}</value_translation> <value_translation type="function">abspath</value_translation>