Mercurial > repos > davidvanzessen > mutation_analysis

diff wrapper.sh @ 52:d3542f87a304 draft

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Uploaded
author davidvanzessen
date Fri, 29 Jan 2016 08:11:31 -0500
parents 8ba6afa1247a
children 7290a88ea202
line wrap: on
line diff
--- a/wrapper.sh	Fri Jan 29 05:42:17 2016 -0500
+++ b/wrapper.sh	Fri Jan 29 08:11:31 2016 -0500
@@ -10,6 +10,7 @@
 functionality=$7
 unique=$8
 naive_output=$9
+filter_unique=${10}
 mkdir $outdir
 
 type="`file $input`"
@@ -57,7 +58,7 @@
 
 
 echo "merging"
-Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique
+Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique}
 
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"