Mercurial > repos > jjohnson > snpeff
changeset 6:eb394dd65c98
Add mutli-select to data managers from Bjoern, filter unique database options in snpEff_download.xml snpEff.xml
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Nov 2013 08:16:11 -0600 |
| parents | 8952990fcab9 |
| children | 0ad9733e22a4 |
| files | data_manager/data_manager_snpEff_databases.py data_manager/data_manager_snpEff_download.py data_manager/data_manager_snpEff_download.xml snpEff.xml snpEff_download.xml |
| diffstat | 5 files changed, 14 insertions(+), 6 deletions(-) [+] |
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--- a/data_manager/data_manager_snpEff_databases.py Wed Nov 27 09:11:32 2013 -0600 +++ b/data_manager/data_manager_snpEff_databases.py Thu Nov 28 08:16:11 2013 -0600 @@ -44,11 +44,14 @@ fields = line.split('\t') if len(fields) >= 2: genome_version = fields[0].strip() - if genome_version.startswith("Genome") or genome_version.startswith("-"): + if genome_version.startswith("Genome") or genome_version.startswith("-"): + continue + #snpeff test genome + if genome_version == '30c2c903' or fields[1].strip() == 'TestCase' or fields[1].strip().startswith('Test_'): continue description = fields[1].strip() + ' : ' + genome_version data_table_entries.append(dict(value=genome_version, name=description)) - data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries + data_manager_dict['data_tables']['snpeff_databases'] = data_table_entries except Exception, e: stop_err( 'Error parsing %s %s\n' % (config,str( e )) ) else:
--- a/data_manager/data_manager_snpEff_download.py Wed Nov 27 09:11:32 2013 -0600 +++ b/data_manager/data_manager_snpEff_download.py Thu Nov 28 08:16:11 2013 -0600 @@ -104,7 +104,8 @@ #Create SnpEff Reference Data - download_database(data_manager_dict, target_directory, options.jar_path,options.config,options.genome_version,options.organism) + for genome_version, organism in zip(options.genome_version.split(','), options.organism.split(',')): + download_database( data_manager_dict, target_directory, options.jar_path, options.config, genome_version, organism ) #save info to json file open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
--- a/data_manager/data_manager_snpEff_download.xml Wed Nov 27 09:11:32 2013 -0600 +++ b/data_manager/data_manager_snpEff_download.xml Thu Nov 28 08:16:11 2013 -0600 @@ -10,7 +10,7 @@ "$out_file" </command> <inputs> - <param name="genome_databases" type="select" label="Genome Version"> + <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version"> <options from_data_table="snpeff_databases"> <filter type="sort_by" column="0" /> </options>
--- a/snpEff.xml Wed Nov 27 09:11:32 2013 -0600 +++ b/snpEff.xml Thu Nov 28 08:16:11 2013 -0600 @@ -93,7 +93,9 @@ <when value="cached"> <param name="genomeVersion" type="select" label="Genome"> <!--GENOME DESCRIPTION--> - <options from_data_table="snpeff_genomedb"/> + <options from_data_table="snpeff_genomedb"> + <filter type="unique_value" column="0" /> + </options> </param> <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> <help>These are available for only a few genomes</help>
--- a/snpEff_download.xml Wed Nov 27 09:11:32 2013 -0600 +++ b/snpEff_download.xml Thu Nov 28 08:16:11 2013 -0600 @@ -9,7 +9,9 @@ </command> <inputs> <param name="genomeVersion" type="select" label="Genome Version"> - <options from_data_table="snpeff_databases"/> + <options from_data_table="snpeff_databases"> + <filter type="sort_by" column="0" /> + </options> </param> </inputs> <outputs>