Elements

Each element used in the workflow must be described within the body. An element description consists of the element name and a set of parameters enclosed in curly braces. A parameter and its value are separated by a colon ‘:’, and different parameters are separated by semicolons ‘;’:

element_name {
    parameter1:value1;
    parameter2:value2;
    ...
}

See, for example, a description of the Read alignment element:

read-msa {
    type:read-msa;
    name:"Read alignment";
    url-in:/home/user/pkinase.sto;
}

Note that the values of the parameters for an element can also be presented in the iterations block. For all elements, the following parameters are defined:

  • type - specifies the type of the element.
  • name - specifies the name of the element. It corresponds to the element’s name in the GUI.
  • .validator - validates the element using the input validator type’s parameters:
    • type - specifies the type of the validator.

For example, this validator ensures that the read sequence element has two or three datasets:

read-sequence {
    type:read-sequence;
    name:"Read Sequence";
    .validator {
        type:datasets-count;
        min:2;
        max:3;
    }
}

For custom elements, there is a special parameter:

  • script - sets the script text of the element, for example:
dump-info {
    type:"Script-Dump sequence info";
    name:"Dump sequence info";
    script {
        out_text=getName(in_sequence) + ": " + size(in_sequence);
    }
}

The list of available parameters depends on the element. Refer to the Workflow Elements chapter to find out the parameters for a particular element. To set a script value for a parameter, use the following form:

parameter_name {
    a script value
};
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