view VCFToolsSlidingWindow/vcfToolsSlidingWindow.sh @ 4:b762ecbe2314 draft

planemo upload

#!/bin/bash

tool_path=$(dirname $0)

filein=$1
fileout_label=$(date "+%Y%m%d%H%M%S")
window=$2
filelog=$3
fileout_taj=$4
fileout_tstv=$5
fileout_windowed=$6
fileout_snp=$7
group=$8
if [ "$group" != "none" ]
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 --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 
mv ${fileout_label}.Tajima.D ${fileout_taj} 
mv ${fileout_label}.TsTv ${fileout_tstv} 
mv ${fileout_label}.windowed.pi ${fileout_windowed}
mv ${fileout_label}.snpden ${fileout_snp} 

if [ "$group" != "none" ] 
then mv ${fileout_label}.fst.txt ${fileout_fst} 
mv ${fileout_label}.fst.by_marker.genes.txt ${fileout_fst_marker} 
mv ${fileout_label}.combined.dtajima.txt ${fileout_taj_combined} 
mv ${fileout_label}.combined.pi.txt ${fileout_windowed_combined}
fi

rm -f ${filein}.vcf ${filein}.vcf.*