diff VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh @ 4:b762ecbe2314 draft

planemo upload

--- a/VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh	Mon Nov 09 05:18:45 2015 -0500
+++ b/VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh	Fri Dec 11 07:35:00 2015 -0500
@@ -4,26 +4,25 @@
 
 filein=$1
 fileout_label=$(date "+%Y%m%d%H%M%S")
-step=$2
-window=$3
-filelog=$4
-fileout_taj=$5
-fileout_tstv=$6
-fileout_windowed=$7
-fileout_snp=$8
-group=$9
+window=$2
+filelog=$3
+fileout_taj=$4
+fileout_tstv=$5
+fileout_windowed=$6
+fileout_snp=$7
+group=$8
 if [ "$group" != "none" ]
-then fileout_fst=${10}
-	fileout_fst_marker=${11}
-	fileout_taj_combined=${12}
-	fileout_windowed_combined=${13}
+then fileout_fst=${9}
+	fileout_fst_marker=${10}
+	fileout_taj_combined=${11}
+	fileout_windowed_combined=${12}
 fi
 
 
 cp $filein ${filein}.vcf 
 if [ "$group" != "none" ] 
-then perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --step $step --window $window --group $group
-else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --step $step --window $window
+then perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --window $window --group $group
+else perl $tool_path/VCFToolsSlidingWindow.pl --input ${filein}.vcf --out $fileout_label --window $window
 fi
         
 mv ${fileout_label}.vcftools.log $filelog