Batch Architect: Design of Batch Templates

David Maddison & Wayne Maddison

The Template Editor for editing Batch File templates appears as follows:

The text entered into the "Text for start of batch file" field will be written once, at the start of the file; the text in "Repeated text, written for each replicate" will be written as many times as there are replicates; the text in "Text for end of batch file" will be written at the end of the file. The following codes included in these fields will be replaced in the batch file as follows:

<name> will be replaced by the text entered in the "base name" field in the Export Matrices & Batch Files or Export Batch Files dialog boxes.
<tree> will be replaced by the Newick formatted text description of the tree chosen in the Export Matrices & Batch Files or Export Batch Files dialog boxes.
<snippet></snippet> surrounding the name of a code snippet will be replaced by the text of the code snippet
<fileExtension> will be replaced by the extension (with dot, if present; e.g., ".nex", ".ss") that Mesquite will write based upon the matrix format.
<matrixFormat> will be replaced by the name of the matrix format (e.g., "NEXUS file")
<random> numValues=n lowerBound=b1 upperBound=b2 type=double|long withReplacement=yes|no </random> will be replaced by n random numbers chosen with a uniform distribution over the range b1 through b2 inclusive, with replacement or not. The numbers are either real numbers (if type=double is chosen) or integers (type=long). For example, <random>numValues=3 lowerBound=1 upperBound=100 type=long withReplacement=no</random> entered in the repeated text field might be replaced by "86 42 23" in one replicate, and "5 73 31" in the next replicate.

For the field "Repeated text, written for each replicate", the following replacement will also be made:

<number> will be replaced by the number of the replicate

For example, consider 5 replicates run with a base name of "matrix" for a template with the following specification:

A file called "commands.nex" would be created by Mesquite that would look like this:

  #NEXUS
  begin paup;
        set autoclose nowarnreset nowarntree nowarntsave;
        execute 'matrix1.nex';
        hs;
        savetrees file = 'maxtrix1.nex';

        execute 'matrix2.nex';
        hs;
        savetrees file = 'matrix2.nex';

        execute 'matrix3.nex';
        hs;
        savetrees file = 'matrix3.nex';

        execute 'matrix4.nex';
        hs;
        savetrees file = 'matrix4.nex';

        execute 'matrix5.nex';
        hs;
        savetrees file = 'matrix5.nex';
  end;

Up to five separate batch files can be specified for any one Batch File Template.

The "Format of Matrices" choice will be ignored if matrices are not being exported (e.g., if Export Batch Files was chosen).