Tablet XML

Tablet supports Tablet XML files, or .tablet files, for specifying sets of data which can be loaded together. If you have Tablet installed you can double click a .tablet file to launch Tablet with the data specified in that file. Alternatively you can drag and drop a .tablet file onto an already open instance of Tablet to load the associated data, or load data using a .tablet file as the argument to Tablet on the command line.

Note

There is no way to open a Tablet XML (.tablet) file from within Tablet, other than by dragging and dropping the file onto Tablet.

Tablet XML Elements

Tablet XML files allow you to specify the following elements, an assembly file, a reference file, an annotation file, a contig and a position. The only required element is an assembly file. The position element only works when paired with a contig element. Below are examples of how to specify each element:

  • Assembly file (required)

    This can be in any of the assembly file formats that Tablet supports.

    <assembly>http://bioinf.hutton.ac.uk/tablet/sample-data/book/example4/Example4.bam</assembly>
    
  • Reference file (optional)

    A fasta formatted reference file.

    <reference>http://bioinf.hutton.ac.uk/tablet/sample-data/book/example4/Example4.fasta</reference>
    
  • Annotation file (optional)

    A gff3 formatted annotation file.

    <annotation>http://bioinf.hutton.ac.uk/tablet/sample-data/book/example4/Example4.gff</annotation>
    
  • Contig (optional)

    This should be the name of a contig in the assembly file.

    <contig>contig_53395</contig>
    
  • Position (optional)

    A position within the specified contig.

    <position>14000</position>
    

Example

<tablet>
        <assembly>http://bioinf.hutton.ac.uk/tablet/sample-data/book/example4/Example4.bam</assembly>
        <reference>http://bioinf.hutton.ac.uk/tablet/sample-data/book/example4/Example4.fasta</reference>
        <annotation>http://bioinf.hutton.ac.uk/tablet/sample-data/book/example4/Example4.gff</annotation>
        <contig>contig_53395</contig>
        <position>14000</position>
</tablet>

This example file can be downloaded by clicking here.