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The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.

The full printed program is also available.
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Thursday, June 29 • 17:30 - 17:36
Improving Your Text Life

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Slides

Authors

James Johnson 1

1 : University of Minnesota Supercomputing Institute  (MSI), 599 Walter Library, 117 Pleasant St. SE Minneapolis, MN 55455 -  United States

Abstract
The Query Tabular Galaxy tool loads any number of tabular datasets into a new or existing SQLite database allowing the full power of a SQL query to produce a new tabular output. Long, complicated workflows of Galaxy text manipulation tools can be replaced by Query Tabular in a single step.

The Query Tabular tool provides default names for tables: t1, t2, etc. and columns: c1, c2, etc., but a user can specify meaningful names for tables and columns. When specifying names for columns, a user can choose to load only those columns that are given names.

Regex functions are added to sqlite connections so that re.search, re.match, and re.replace functions are available for use in the SQL query.

Line filters can be applied while reading tabular input files to include, exclude, or modify lines before entering the values as rows in the database table. A column replace line filter can use a regex to change a date value to the SQLite recognized format. A normalize filter can convert list fields in the input to first normal form with an individual list item per row.



Presenters
avatar for James Johnson

James Johnson

Minnesota Supercomputing Institute, University of Minnesota



Thursday June 29, 2017 17:30 - 17:36
Einstein Auditorium Le Corum, Level 0

Attendees (10)