It allows writing a GMQL query directly in text form and send it to the GMQL system to be compiled and executed, and in this second case it imports the resulting dataset into the current history. This has been thought as a tool for advanced users who already knows GMQL and its syntax. See the linked GMQL documentation about it.

What it does

Given a GMQL query in plain text, or a GMQL query saved in the current Galaxy history (gmql_query), requires its compilation or execution.

• Compile query: send the query to be compiled on the GMQL system. It returns the compilation log.
• Run query: send the query to be run on the GMQL system. User can choose to automatically import the resulting dataset or not, and the output format. It returns the log generated by the system, an updated list of the user dataset, and the two collections corresponding to the result datasets samples and metadata, respectively.

A gmql_user authentication token is required for every action.

Output formats

• GTF: General feature format, fields are: seqname, source, feature, start (1-based), end, score, strand, frame, attribute
• GDM (Tab Delimited): the Genomic Data Model developed within the GMQL project. Fields are at least: chr, start (0-based), stop, strand (regions coordinates) plus an arbitrary set of additional attributes.