Commit 75269563 authored by aknecht2's avatar aknecht2
Browse files

Updated 3 things: 1st changed pepr arguments to be a list with a separator. ...

Updated 3 things: 1st changed pepr arguments to be a list with a separator.  Updated argument parsing to allow joining list arguments with another value.  Updated conf to allow separator as a valid argument option.
parent 4b894ba5
......@@ -120,7 +120,7 @@ argument_types = {
# Defines information about arguments
argument_keys = {
"required": ["type", "changeable", "has_value"],
"optional": ["required", "default", "file_type", "path"]
"optional": ["required", "default", "file_type", "path", "separator"]
}
# workflow_job keys
......
......@@ -20,17 +20,23 @@ pepr_callpeak:
command: pepr
arguments:
- "-c":
type: file
type: list
separator: ","
changeable: false
required: true
has_value: true
default: "$inputs.0,$inputs.0"
default:
- $inputs.0
- $inputs.0
- "-i":
type: file
type: list
separator: ","
changeable: false
required: true
has_value: true
default: "$inputs.1,$inputs.1"
default:
- $inputs.1
- $inputs.1
- "-n":
type: string
changeable: true
......
......@@ -514,9 +514,12 @@ class WorkflowJob(object):
arg_list.append(arg_name)
arg_list.append(add_value)
elif isinstance(add_value, list):
arg_list.append(arg_name)
for f in add_value:
arg_list.append(f)
if "separator" in arg_info:
arg_list.append(arg_info["seperator"].join(add_value))
else:
arg_list.append(arg_name)
for f in add_value:
arg_list.append(f)
else:
arg_list.append("%s %s" % (arg_name, add_value))
else:
......
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