Elements

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

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

For custom elements there is 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 parameters available depend on an 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
};