Mercurial > repos > dfornika > data_manager_build_mob_suite_database
changeset 0:d51005ef511c draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_mob_suite_database/ commit 77f160b9d557a33ee830c2aff93d423ce2d6b815-dirty
| author | dfornika |
|---|---|
| date | Fri, 24 May 2019 15:19:05 -0400 |
| parents | |
| children | 135a2f002c6a |
| files | data_manager/mob_suite_build_database.py data_manager/mob_suite_build_database.xml data_manager_conf.xml tool-data/mob_suite_databases.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 143 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/mob_suite_build_database.py Fri May 24 15:19:05 2019 -0400 @@ -0,0 +1,84 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import datetime +import errno +import json +import os +import string +import subprocess +import sys + + +DATA_TABLE_NAME = "mob_suite_databases" + + +def mob_suite_build_database_mob_init(mob_suite_args, target_directory, data_table_name=DATA_TABLE_NAME): + + now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") + + database_value = "_".join([ + ]) + + database_name = " ".join([ + ]) + + database_path = database_value + + args = [ + ] + + run(['mob_init'] + args, target_directory) + + data_table_entry = { + "data_tables": { + data_table_name: [ + { + "value": database_value, + "name": database_name, + "path": database_path, + } + ] + } + } + + return data_table_entry + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('data_manager_json') + parser.add_argument( '--threads', dest='threads', default=1, help='threads' ) + parser.add_argument( '--mode', dest='mode', default=1, help='database construction mode' ) + args = parser.parse_args() + + data_manager_input = json.loads(open(args.data_manager_json).read()) + + target_directory = data_manager_input['output_data'][0]['extra_files_path'] + + try: + os.mkdir( target_directory ) + except OSError as exc: + if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): + pass + else: + raise + + data_manager_output = {} + + if str(args.mode) == 'mob_init': + mob_suite_args = {} + data_manager_output = mob_suite_build_database_mob_init( + mob_suite_args, + target_directory, + ) + else: + sys.exit("Invalid database construction mode") + + open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/mob_suite_build_database.xml Fri May 24 15:19:05 2019 -0400 @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<tool id="mob_suite_build_database" name="MOB-Suite Database Builder" tool_type="manage_data" version="1.4.9.1"> + <description>database builder</description> + <requirements> + <requirement type="package" version="1.4.9.1">mob_suite</requirement> + </requirements> + <version_command>echo '1.4.9.1'</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/mob_suite_build_database.py' + '${out_file}' + --threads \${GALAXY_SLOTS:-1} + --mode ${mode.mode} + ]]> + </command> + <inputs> + <conditional name="mode"> + <param name="mode" type="select" multiple="false" label="Mode"> + <option value="mob_init">Initialize Standard Database (mob_init)</option> + </param> + <when value="mob_init"> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <help> + </help> + <citations> + <citation type="doi">10.1099/mgen.0.000206</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Fri May 24 15:19:05 2019 -0400 @@ -0,0 +1,18 @@ +<data_managers> + <data_manager tool_file="data_manager/mash_build_mob_suite_database.xml" id="mob_suite_build_database" version="1.0"> + <data_table name="mob_suite_databases"> + <output> + <column name="value"/> + <column name="name"/> + <column name="path" output_ref="out_file"> + <move type="file"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mob_suite_databases/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mob_suite_databases/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri May 24 15:19:05 2019 -0400 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Mash sketches in the required format --> + <table name="mob_suite_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/mob_suite_databases.loc" /> + </table> +</tables>