| Previous changeset 1:955a8d483fa3 (2018-07-10) Next changeset 3:cb0fa3584aeb (2018-10-09) |
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Commit message:
Uploaded |
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modified:
data_manager/data_manager_fetch_gff.py data_manager/data_manager_fetch_gff.xml data_manager_conf.xml tool-data/all_gff.loc.sample |
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added:
tool-data/representative_gff.loc.sample |
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| diff -r 955a8d483fa3 -r c57bd7f3fb46 data_manager/data_manager_fetch_gff.py --- a/data_manager/data_manager_fetch_gff.py Tue Jul 10 05:30:23 2018 -0400 +++ b/data_manager/data_manager_fetch_gff.py Tue Jul 10 10:55:47 2018 -0400 |
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| @@ -39,19 +39,20 @@ def get_dbkey_dbname_id_name( params, dbkey_description=None ): - dbkey = params['param_dict']['dbkey_source']['dbkey'] +# dbkey = params['param_dict']['dbkey_source']['dbkey'] #TODO: ensure sequence_id is unique and does not already appear in location file sequence_id = params['param_dict']['sequence_id'] if not sequence_id: sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead? - if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new': - dbkey_name = params['param_dict']['dbkey_source']['dbkey_name'] - if not dbkey_name: - dbkey_name = dbkey - else: - dbkey_name = None - +# if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new': +# dbkey_name = params['param_dict']['dbkey_source']['dbkey_name'] +# if not dbkey_name: +# dbkey_name = dbkey +# else: +# dbkey_name = None + dbkey = params['param_dict']['dbkey'] + dbkey_name = dbkey_description sequence_name = params['param_dict']['sequence_name'] if not sequence_name: sequence_name = dbkey_description @@ -360,14 +361,8 @@ #sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params ) - dbkey_dict = None - if dbkey_name: - #do len calc here - #len_base_name = "%s.len" % ( dbkey ) - #compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True ) - dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path='' ) - return [ ( '__dbkeys__', dbkey_dict ), ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] + return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] def compute_fasta_length( fasta_file, out_file, keep_first_word=False ): @@ -407,15 +402,7 @@ fasta_base_filename = "%s.fa" % sequence_id fasta_filename = os.path.join( target_directory, fasta_base_filename ) os.symlink( input_filename, fasta_filename ) - - dbkey_dict = None - if dbkey_name: - #do len calc here - len_base_name = "%s.len" % ( dbkey ) - compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True ) - dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name ) - - return [ ( '__dbkeys__', dbkey_dict ), ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] + return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ] REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory ) |
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| diff -r 955a8d483fa3 -r c57bd7f3fb46 data_manager/data_manager_fetch_gff.xml --- a/data_manager/data_manager_fetch_gff.xml Tue Jul 10 05:30:23 2018 -0400 +++ b/data_manager/data_manager_fetch_gff.xml Tue Jul 10 10:55:47 2018 -0400 |
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| @@ -3,11 +3,7 @@ <command><![CDATA[ python "$__tool_directory__"/data_manager_fetch_gff.py "${out_file}" --type $file_type - #if str( $dbkey_source.dbkey_source_selector ) == 'existing': - --dbkey_description ${ dbkey_source.dbkey.get_display_text() } - #else - --dbkey_description "${ dbkey_source.dbkey_name or $dbkey_source.dbkey }" - #end if + --dbkey_description ${ dbkey.get_display_text() } ]]></command> <inputs> @@ -16,19 +12,7 @@ <option value="full">GFF with complete features</option> </param> - <conditional name="dbkey_source"> - <param name="dbkey_source_selector" type="select" label="Use existing dbkey or create a new one."> - <option value="existing" selected="True">Existing</option> - <option value="new">New</option> - </param> - <when value="existing"> - <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> - </when> - <when value="new"> - <param type="text" name="dbkey" value="" label="dbkey" optional="False" /> - <param type="text" name="dbkey_name" value="" label="Display name for dbkey" /> - </when> - </conditional> + <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> <param type="text" name="sequence_name" value="" label="Name of sequence" /> <param type="text" name="sequence_id" value="" label="ID for sequence" /> <conditional name="reference_source"> |
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| diff -r 955a8d483fa3 -r c57bd7f3fb46 data_manager_conf.xml --- a/data_manager_conf.xml Tue Jul 10 05:30:23 2018 -0400 +++ b/data_manager_conf.xml Tue Jul 10 10:55:47 2018 -0400 |
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| @@ -31,20 +31,5 @@ </column> </output> </data_table> - - <data_table name="__dbkeys__"> - <output> - <column name="value" /> - <column name="name" /> - <column name="len_path" output_ref="out_file"> - <move type="file"> - <source>${len_path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/len/${len_path}</target> - </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/len/${len_path}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> </data_manager> </data_managers> |
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| diff -r 955a8d483fa3 -r c57bd7f3fb46 tool-data/all_gff.loc.sample --- a/tool-data/all_gff.loc.sample Tue Jul 10 05:30:23 2018 -0400 +++ b/tool-data/all_gff.loc.sample Tue Jul 10 10:55:47 2018 -0400 |
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| @@ -1,3 +1,3 @@ #The all_gff.loc file has this format: # -#<id> <dbkey> <name> <path_to_gff_file> +#<unique_build_id> <dbkey> <display_name> <path_to_gff_file> |
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| diff -r 955a8d483fa3 -r c57bd7f3fb46 tool-data/representative_gff.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/representative_gff.loc.sample Tue Jul 10 10:55:47 2018 -0400 |
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| @@ -0,0 +1,3 @@ +#The representative_gff.loc file has this format: +# +#<unique_build_id> <dbkey> <display_name> <path_to_gff_file> |