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