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 ‘;’:
Code Block |
---|
element_name {
parameter1:value1;
parameter2:value2;
...
} |
See, for example, a description of the Read alignment element:
Code Block |
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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 by the input validator type's parameters:
- type - specifies the type of the validator.
- type - specifies the type of the validator.
For example this validator validate that the read sequence element has two or three datasets:
Code Block |
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read-sequence {
type:read-sequence;
name:"Read Sequence";
.validator {
type:datasets-count;
min:2;
max:3;
}
} |
For custom elements there is special parameter:
- script - sets the script text of the element, for example:
- script - sets the script text of the element, for example:
Code Block |
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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:
Code Block |
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parameter_name {
a script value
}; |