#! /bin/sh

#Arguments :
#$1=targetFile(the list of files) 
#$2=with or without header
#$3=with or without replicates
#$4=OUT_HTML.html
#$5=OUT_HTML images directory
#$6=OUT_complete.xls
#$7=OUT_up.xls
#$8=OUT_down.xls

#run example: 
#bash deseq.sh DESeqTools/targetTest.txt 1 1 testOUT_HTML.html /tmp/ testOUT_complet.xls testOUT_up.xls testOUT_down.xls

#echo $5
#mkdir -p $5 #First, create the images tmp directory given by Galaxy, -p option can create the parent directory which dosen't exist.

mkdir -p $5
MY_PATH=`dirname $0` 
cat $MY_PATH/DESeqTools/anadiffGenes2conds.R | R --slave --args $1 $2 $3 $4 $5 $6 $7 $8 $0 < $MY_PATH/DESeqTools/anadiffGenes2conds.R