Commit 6e23233e authored by aknecht2's avatar aknecht2
Browse files

Fixed arguments for pepr peak calling. Updated params in peak_call module to...

Fixed arguments for pepr peak calling.  Updated params in peak_call module to correctly reflect the output files produced by hidden domains.
parent 0a6048fd
...@@ -339,7 +339,7 @@ peak_call: ...@@ -339,7 +339,7 @@ peak_call:
prefix: prefix:
param_name: prefix param_name: prefix
outputs: outputs:
result.bed: analysis.bed:
param_name: result_peaks param_name: result_peaks
vis.bed: vis.bed:
param_name: enriched_bins param_name: enriched_bins
...@@ -351,7 +351,7 @@ peak_call: ...@@ -351,7 +351,7 @@ peak_call:
param_name: treatment_bins param_name: treatment_bins
- hiddendomains_format: - hiddendomains_format:
inputs: inputs:
result.bed: analysis.bed:
param_name: result_peaks param_name: result_peaks
outputs: outputs:
results_sorted.bed: results_sorted.bed:
......
...@@ -20,7 +20,7 @@ pepr_callpeak: ...@@ -20,7 +20,7 @@ pepr_callpeak:
command: PePr command: PePr
arguments: arguments:
- "-c": - "-c":
type: list type: file_list
separator: "," separator: ","
changeable: false changeable: false
required: true required: true
...@@ -29,7 +29,7 @@ pepr_callpeak: ...@@ -29,7 +29,7 @@ pepr_callpeak:
- $control.bed - $control.bed
- $control.bed - $control.bed
- "-i": - "-i":
type: list type: file_list
separator: "," separator: ","
changeable: false changeable: false
required: true required: true
...@@ -54,18 +54,11 @@ pepr_callpeak: ...@@ -54,18 +54,11 @@ pepr_callpeak:
changeable: true changeable: true
required: false required: false
has_value: true has_value: true
default: 10
- "-w": - "-w":
type: numeric type: numeric
changeable: true changeable: true
required: false required: false
has_value: true has_value: true
default: 100
- "--diff":
type: string
changeable: false
required: true
has_value: false
- "--threshold": - "--threshold":
type: string type: string
changeable: true changeable: true
...@@ -89,7 +82,6 @@ pepr_callpeak: ...@@ -89,7 +82,6 @@ pepr_callpeak:
changeable: true changeable: true
required: false required: false
has_value: true has_value: true
default: 10000000
- "--num-processors": - "--num-processors":
type: numeric type: numeric
changeable: true changeable: true
......
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