Commit 716ec5b1 authored by aknecht2's avatar aknecht2
Browse files

Updated r_spp yaml & wrapper to have = within the job args.

parent 99c8ab3a
...@@ -14,47 +14,47 @@ r_spp_nodups: ...@@ -14,47 +14,47 @@ r_spp_nodups:
type: file type: file
command: r command: r
arguments: arguments:
- "-c": - "-c=":
changeable: false changeable: false
required: true required: true
has_value: true has_value: true
default: $inputs.0 default: $inputs.0
- "-i": - "-i=":
changeable: false changeable: false
required: true required: true
has_value: true has_value: true
default: $inputs.1 default: $inputs.1
- "-npeak": - "-npeak=":
changeable: true changeable: true
required: false required: false
has_value: true has_value: true
default: 300000 default: 300000
- "-odir": - "-odir=":
changeable: false changeable: false
required: true required: true
has_value: true has_value: true
default: . default: .
- "-speak": - "-speak=":
changeable: true changeable: true
required: false required: false
has_value: true has_value: true
default: 110 default: 110
- "-savn": - "-savn=":
changeable: false changeable: false
required: true required: true
has_value: true has_value: true
default: $outputs.0 default: $outputs.0
- "-savp": - "-savp=":
changeable: false changeable: false
required: true required: true
has_value: true has_value: true
default: $outputs.1 default: $outputs.1
- "-out": - "-out=":
changeable: false changeable: false
required: true required: true
has_value: true has_value: true
default: $outputs.2 default: $outputs.2
- "-fdr": - "-fdr=":
changeable: true changeable: true
required: false required: false
has_value: true has_value: true
......
...@@ -2,11 +2,7 @@ ...@@ -2,11 +2,7 @@
. /util/opt/lmod/lmod/init/profile . /util/opt/lmod/lmod/init/profile
module load R spp module load R spp
newargs=() # Remove extra space after equal signs
while (( ${#@} )) # to make r_spp_nodups happy.
do args=`echo $@ | sed -e 's/= /=/g'`
newargs+=("$1=$2") Rscript ${SPP_NODUPS} $args
shift
shift
done
Rscript ${SPP_NODUPS} "${newargs[@]/#/}"
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