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comparison bsmap_wrapper.sh @ 3:91e88de226a3 draft

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author eiriche
date Thu, 29 Nov 2012 10:10:16 -0500
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2:41f30b042bac 3:91e88de226a3
1 #!/bin/bash
2 #
3 # Galaxy wrapper for BSMAP
4 # Written by Eugen Eirich @ Institute for Molecular Biology Mainz
5 #
6
7 set -e
8
9 #get parameters
10
11 until [ $# -eq 0 ]
12 do
13 case $1 in
14 ref=*)
15 ref=${1#ref=}
16 ;;
17 library=*)
18 library=${1#library=}
19 ;;
20 unpaired=*)
21 unpaired=${1#unpaired=}
22 ;;
23 mapped=*)
24 mapped=${1#mapped=}
25 ;;
26 fullparam=*)
27 fullparam=${1#fullparam=}
28 ;;
29 mate1=*)
30 mate1=${1#mate1=}
31 ;;
32 mate2=*)
33 mate2=${1#mate2=}
34 ;;
35 qual=*)
36 qual="-z ${1#qual=}"
37 ;;
38 threshold=*)
39 threshold="-q ${1#threshold=}"
40 ;;
41 lowqual=*)
42 lowqual="-f ${1#lowqual=}"
43 ;;
44 adapter=*)
45 adapter=${1#adapter=}
46 ;;
47 firstn=*)
48 firstn="-L ${1#firstn=}"
49 ;;
50 repeat_reads=*)
51 repeat_reads="-r ${1#repeat_reads=}"
52 ;;
53 seed_size=*)
54 seed_size="-s ${1#seed_size=}"
55 ;;
56 mismatch=*)
57 mismatch="-v ${1#mismatch=}"
58 ;;
59 equal_best=*)
60 equal_best="-w ${1#equal_best=}"
61 ;;
62 start=*)
63 start="-B ${1#start=}"
64 ;;
65 end=*)
66 end="-E ${1#end=}"
67 ;;
68 index_interval=*)
69 index_interval="-I ${1#index_interval=}"
70 ;;
71 seed_random=*)
72 seed_random=${1#seed_random=}
73 ;;
74 rrbs=*)
75 rrbs=${1#rrbs=}
76 ;;
77 mode=*)
78 mode="-n ${1#mode=}"
79 ;;
80 align_info=*)
81 align_info=${1#align_info=}
82 ;;
83 maxinsert=*)
84 maxinsert="-x ${1#maxinsert=}"
85 ;;
86 mininsert=*)
87 mininsert="-m ${1#mininsert=}"
88 ;;
89 summary=*)
90 summary=${1#summary=}
91 ;;
92 esac
93 shift
94 done
95
96
97 if [ "$rrbs" != "" ]
98 then
99 rrbs="-D $rrbs"
100 fi
101
102 if [ "$align_info" != "" ]
103 then
104 align_info="-M $align_info"
105 fi
106
107 if [ "$adapter" != "" ]
108 then
109 adapter="-A $adapter"
110 fi
111
112 if [ "$seed_random" != "" ]
113 then
114 seed_random="-S $seed_random"
115 fi
116
117
118 if [ "$library" == "single" ]
119 then
120 if [ "$fullparam" == 'false' ]
121 then
122 bsmap -a $mate1 -d $ref -o $mapped -R -r 0 -p 4 > $summary
123 else
124 bsmap -a $mate1 -d $ref -o $mapped -R -r 0 -p 4 $qual $threshold $lowqual $adapter $firstn $repeat_reads $seed_size $mismatch $equal_best $start $end $index_interval $mode > $summary
125 fi
126 else
127 if [ "$fullparam" == 'false' ]
128 then
129 bsmap -a $mate1 -b $mate2 -2 $unpaired -d $ref -o $mapped -R -r 0 -p 4 > $summary
130 else
131 bsmap -a $mate1 -b $mate2 -2 $unpaired -d $ref -o $mapped -R -r 0 -p 4 $qual $threshold $lowqual $adapter $firstn $repeat_reads $seed_size $mismatch $equal_best $start $end $index_interval $mode $maxinsert $mininsert > $summary
132 fi
133 fi