diff --git a/README.rst b/README.rst index 4483865..a2d9f2d 100644 --- a/README.rst +++ b/README.rst @@ -25,12 +25,11 @@ ENASearch is easy to use $ enasearch --help Usage: enasearch [OPTIONS] COMMAND [ARGS]... - - + Options: - - --help Show this message and exit. - + --version Show the version and exit. + -h, --help Show this message and exit. + Commands: get_analysis_fields Get analysis fields get_display_options Get display options @@ -51,36 +50,34 @@ ENASearch is easy to use $ enasearch search_data --help Usage: enasearch search_data [OPTIONS] - Search data given a query - Options: - --free_text_search Use free text search, otherwise the data warehouse - is used - --query TEXT Query string, made up of filtering conditions, - joined by logical ANDs, ORs and NOTs and bound by - double quotes; the filter fields for a query are - accessible with get_filter_fields and the type of - filters with get_filter_types [required] - --result TEXT Id of a result (accessible with get_results) - [required] - --display TEXT Display option to specify the display format - (accessible with get_display_options) [required] - --download TEXT Download option to specify that records are to be - saved in a file (used with file option, list - accessible with get_download_options) - --file PATH File to save the content of the search (used with - download option) - --fields TEXT Fields to return (accessible with - get_returnable_fields, used only for report as - display value) [multiple] - --sortfields TEXT Fields to sort the results (accessible with - get_sortable_fields, used only for report as display - value) [multiple] - --offset INTEGER RANGE First record to get (used only for display different - of fasta and fastq - --length INTEGER RANGE Number of records to retrieve (used only for display - different of fasta and fastq - --help Show this message and exit. + --free_text_search Use free text search, otherwise the data warehouse + is used + --query TEXT Query string, made up of filtering conditions, + joined by logical ANDs, ORs and NOTs and bound by + double quotes; the filter fields for a query are + accessible with get_filter_fields and the type of + filters with get_filter_types [required] + --result TEXT Id of a result (accessible with get_results) + [required] + --display TEXT Display option to specify the display format + (accessible with get_display_options) [required] + --download TEXT Download option to specify that records are to be + saved in a file (used with file option, list + accessible with get_download_options) + --file PATH File to save the content of the search (used with + download option) + --fields TEXT Fields to return (accessible with + get_returnable_fields, used only for report as + display value) [multiple or comma-separated] + --sortfields TEXT Fields to sort the results (accessible with + get_sortable_fields, used only for report as display + value) [multiple or comma-separated] + --offset INTEGER RANGE First record to get (used only for display different + of fasta and fastq + --length INTEGER RANGE Number of records to retrieve (used only for display + different of fasta and fastq + -h, --help Show this message and exit. It can also be used as a Python library: