Mercurial > repos > iuc > data_manager_gemini_database_downloader
changeset 3:172815da3d41 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
| author | iuc |
|---|---|
| date | Tue, 04 Apr 2017 18:09:05 -0400 |
| parents | 345412d58d75 |
| children | fe5a9a7d95b0 |
| files | data_manager/data_manager_gemini_download.py data_manager/data_manager_gemini_download.xml tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 4 files changed, 17 insertions(+), 31 deletions(-) [+] |
line wrap: on
line diff
--- a/data_manager/data_manager_gemini_download.py Thu Feb 18 08:49:06 2016 -0500 +++ b/data_manager/data_manager_gemini_download.py Tue Apr 04 18:09:05 2017 -0400 @@ -1,32 +1,31 @@ #!/usr/bin/env python -import sys -import os +import datetime import json -import shlex -import datetime +import os import subprocess +import sys + def main(): - today = datetime.date.today() params = json.loads( open( sys.argv[1] ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) - ret = subprocess.check_call( cmd, shell=True ) + subprocess.check_call( cmd, shell=True ) data_manager_dict = { - 'data_tables': - {'gemini_databases': [ - {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } - ] - } - } + 'data_tables': { + 'gemini_databases': [ + {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } + ] + } + } - #save info to json file + # save info to json file with open( sys.argv[1], 'wb' ) as out: out.write( json.dumps( data_manager_dict ) ) + if __name__ == "__main__": main() -
--- a/data_manager/data_manager_gemini_download.xml Thu Feb 18 08:49:06 2016 -0500 +++ b/data_manager/data_manager_gemini_download.xml Tue Apr 04 18:09:05 2017 -0400 @@ -3,12 +3,8 @@ <requirements> <requirement type="package" version="0.18.1">gemini</requirement> </requirements> - <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> - <command interpreter="python"> - data_manager_gemini_download.py "$out_file" + <command detect_errors="exit_code"> + python '$__tool_directory__/data_manager_gemini_download.py' '$out_file' </command> <inputs> <param name="cadd" type="boolean" truevalue="--extra cadd_score" falsevalue="" checked="True" @@ -17,20 +13,17 @@ label="Download GERP for GEMINI database annotation" help="(--extra gerp_bp)"/> </inputs> <outputs> - <data name="out_file" format="data_manager_json" label="${tool.name}"/> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> </outputs> <tests> </tests> <help> - This tool downloads the GEMINI databases. For details about this tool, please go to http://gemini.readthedocs.org - </help> <citations> <citation type="doi">10.1371/journal.pcbi.1003153</citation> - <yield /> </citations> </tool>
--- a/tool_data_table_conf.xml.sample Thu Feb 18 08:49:06 2016 -0500 +++ b/tool_data_table_conf.xml.sample Tue Apr 04 18:09:05 2017 -0400 @@ -1,5 +1,5 @@ <tables> - <table name="gemini_databases" comment_char="#"> + <table name="gemini_databases" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/gemini_databases.loc" /> </table>
--- a/tool_dependencies.xml Thu Feb 18 08:49:06 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="gemini" version="0.18.1"> - <repository changeset_revision="be869e11582f" name="package_gemini_0_18_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>