Commit dae29819 authored by Natasha Pavlovikj's avatar Natasha Pavlovikj
Browse files

PePr updates

parent 75269563
This diff is collapsed.
......@@ -32,7 +32,7 @@ class PeakCallGenerator(ModuleGenerator):
"peakranger": self._peakranger,
"zerone": self._zerone,
"hiddendomains": self._hiddendomains,
"pepr": self._hiddendomains
"pepr": self._pepr
}
self.call_pairs = {}
if debug:
......@@ -170,7 +170,9 @@ class PeakCallGenerator(ModuleGenerator):
call_pair = self.call_pairs[result.full_name]
inputs = {
"control.bed": call_pair[0].full_name,
"signal.bed": call_pair[1].full_name
"signal.bed": call_pair[1].full_name,
"prefix": result.prefix,
"peak_type": run.peak_type
}
additional_inputs = {}
return (self.get_markers(run), inputs, additional_inputs)
......
......@@ -308,19 +308,20 @@ peak_call:
type: file
final_result: true
- pepr[tool]:
- broad[peak_type]:
- pepr_callpeak:
inputs:
- control.bed:
type: file
- signal.bed:
type: file
additional_inputs: null
outputs:
- pepr_result.bed:
type: file
final_result: true
- pepr_parameters.txt:
type: file
- pepr_log.txt:
type: file
- pepr_callpeak:
inputs:
- control.bed:
type: file
- signal.bed:
type: file
- prefix:
type: string
- peak_type:
type: string
additional_inputs: null
outputs:
- pepr_result.bed:
type: file
final_result: true
- pepr_parameters.txt:
type: file
......@@ -6,6 +6,10 @@ pepr_callpeak:
- name: signal
type: file
file_type: bed
- name: prefix
type: string
- name: peak_type
type: string
additional_inputs: null
outputs:
- name: pepr_result
......@@ -14,9 +18,6 @@ pepr_callpeak:
- name: pepr_parameters
type: file
file_type: txt
- name: pepr_log
type: file
file_type: txt
command: pepr
arguments:
- "-c":
......@@ -38,11 +39,11 @@ pepr_callpeak:
- $inputs.1
- $inputs.1
- "-n":
type: string
type: file
changeable: true
required: false
required: true
has_value: true
default: "NA"
default: $inputs.2
- "-f":
type: string
changeable: true
......@@ -62,9 +63,9 @@ pepr_callpeak:
has_value: true
default: 100
- "--diff":
type: boolean
changeable: true
required: false
type: string
changeable: false
required: true
has_value: false
- "--threshold":
type: string
......@@ -77,7 +78,7 @@ pepr_callpeak:
changeable: true
required: true
has_value: true
default: "broad"
default: "$inputs.3"
- "--normalization":
type: string
changeable: true
......
......@@ -25,7 +25,7 @@ class RunParser(object):
self.yaml_data = yaml.load(rh)
self._load_runs(mdb)
except yaml.YAMLError as e:
self.err += "Error parsing run template file [%s]: %s.\n" % (self.run_file, e)
self.errors.append("Error parsing run template file [%s]: %s.\n" % (self.run_file, e))
return
def is_valid(self):
......
No preview for this file type
......@@ -514,14 +514,13 @@ class WorkflowJob(object):
arg_list.append(arg_name)
arg_list.append(add_value)
elif isinstance(add_value, list):
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)
arg_list.append(arg_name)
for i,f in enumerates(add_value):
arg_list.append(f)
if "separator" in arg_info and i != len(add_value) - 1:
arg_list.append(arg_info["separator"])
else:
arg_list.append("%s %s" % (arg_name, add_value))
else:
arg_list.append(add_value)
return arg_list
return arg_list
\ No newline at end of file
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