Mercurial > repos > dereeper > sniplay

comparison VCF2Hapmap/vcf2FastaAndHapmap.sh @ 4:10627af23f10 draft

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planemo upload
author gandres
date Tue, 15 Dec 2015 05:18:02 -0500
parents 420b57c3c185
children
comparison
equal deleted inserted replaced
3:345f88a8f483 4:10627af23f10
3 tool_path=$(dirname $0) 3 tool_path=$(dirname $0)
4 4
5 5
6 6
7 filein=$1 7 filein=$1
8 fileout_label=$2 8 fileout_label=$(date "+%Y%m%d%H%M%S")
9 fileout=$3 9 fileout=$2
10 option=$4 10 option=$3
11 11
12 option_text='' 12 option_text=''
13 13
14 14
15 if [ "$option" != "none" ] 15 if [ "$option" != "none" ]
16 then fileout_seq=$5 16 then fileout_seq=$4
17 fileout_fa1=$6 17 fileout_fa1=$5
18 filefasta=$7 18 filefasta=$6
19 if [ "$option" == "fasta_gff" ] 19 if [ "$option" == "fasta_gff" ]
20 then filegff=$8 20 then filegff=$7
21 fi 21 fi
22 fi 22 fi
23 23
24 if [ "$option" == "fasta" ] 24 if [ "$option" == "fasta" ]
25 then option_text="--reference $filefasta" 25 then option_text="--reference $filefasta"