Mercurial > repos > davidvanzessen > mutation_analysis

diff wrapper.sh @ 66:88e0e7665086 draft

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Uploaded
author davidvanzessen
date Wed, 06 Apr 2016 05:54:13 -0400
parents 0fdd90f7c654
children 7acdcd5c52ef
line wrap: on
line diff
--- a/wrapper.sh	Mon Apr 04 04:25:46 2016 -0400
+++ b/wrapper.sh	Wed Apr 06 05:54:13 2016 -0400
@@ -11,6 +11,7 @@
 unique=$8
 naive_output=$9
 filter_unique=${10}
+class_filter=${11}
 mkdir $outdir
 
 echo "---------------- read parameters ----------------"
@@ -78,7 +79,7 @@
 echo "---------------- merge_and_filter.r ----------------"
 echo "---------------- merge_and_filter.r ----------------<br />" >> $output
 
-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}
+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} ${class_filter}
 
 echo "---------------- mutation_analysis.r ----------------"
 echo "---------------- mutation_analysis.r ----------------<br />" >> $output