parameters

parameters are typed name/value pairs used to specify user preferences on command invocation (termed "executionParameters"), as well as to store input and output values (termed "inputParameters" and "outputParameters" respectively) associated with action execution. Parameters have a value and a defaultValue. When a parameter is referenced, its defaultValue will be used, if it has no value specified.
 
Parameter value and defaultValue fields may be a constant, or they can be an expression that combines constants and/or other parameter values that are referenced by name.
 
Parameters define the following fields
 

 field name

 type

 definition

 name

string

parameter name, which must start with an _ or alphabetic and be followed by zero or more alphanumeric or _ characters. parameter names are unique within the executionParameters, and unique within the context of an action.

 description     string  describes the parameter
 type  string
  •  Long
    An 64 bit signed integer. For example 3412,      -7645
  • Boolean
    A logical value. It is represented as a string as either "true" or "false" and as an integer or float as "1" or "0"
  • Double
    A 64-bit double precision floating point value. For example 3.14159, 1.0E-9
  • String
    A string constant. For example "hello world". Note that if Strings are defined inside a JSON value definition it is necessary to escape the " character and enter it as \". See the example of Escaping Strings in Expressions for more details.
  • Secret
    A string constant with contents that should be not plainly displayed or communicated. For example "dont display me"
  • List
    A vector of typed values [ "now", "is", "the", "time" ]
 value  string  Specifies the parameter value, either as a constant or expression
 defaultValue  string  Specifies the parameter default contant or expression which is used if the value field has not been defined.

 

Figure 1. Example 

"inputParameters":[
    {
        "name":"command",
        "description":"Shell command",
        "type":"String",
        "value":"cp input.file output.file; ls -l input.file output.file"
    },
    {
        "name":"agentBaseUrl",
        "type":"String",
        "value":"$<fileCopier.agentBaseUrl>"
        },
    {
        "name":"n",
        "description":"Number of instances",
        "type":"Long",
        "value":"($<cores>+7)/8",

    }

],

 
 
 
Figure 2. Another Example 

"executionParameters" : [{
    "name" : "e",
    "description" : "depth of coverage for even sampling. 0 to disable",
    "type" : "Long",
    "defaultValue" : "0"
 },
 {
    "name" : "keep_all_samples",
    "description" : "chose the sampling depth to force retaining all samples rather than guessing a sampling depth which may favor keeping more sequences while dropping some samples",
    "type" : "Boolean",
    "defaultValue" : "false"
  },
  {
    "name" : "c",
    "description" : "the categories to compare (for otu_category_significance,supervised_learning.py, and cluster_quality.py steps). Specify - to skip.",
    "type" : "String",
    "defaultValue" : "-"
  },
  {
    "name" : "suppress_split_libraries",
    "description" : "skip demultiplexing/quality filtering (i.e. split_libraries) - this assumes that sequence identifiers are in post-split_libraries format (i.e. sampleID_seqID)",
    "type" : "Boolean",
    "defaultValue" : "false"
  }],

 
 
 
 
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