Mercurial > repos > dawe > srf2fastq
comparison srf2fastq/srf2fastq.sh @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
---|---|
date | Tue, 07 Jun 2011 17:48:05 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:d901c9f41a6a |
---|---|
1 #!/bin/sh | |
2 | |
3 #change this if the path is different | |
4 convert=/usr/local/bin/srf2fastq | |
5 | |
6 srf_file=$1 | |
7 use_filter=$2 | |
8 use_paired=$3 | |
9 fastq_file1=$4 | |
10 fastq_file2=$5 | |
11 options='-c ' | |
12 | |
13 if [ $use_filter == 'Y' ] | |
14 then | |
15 options="$options -C" | |
16 fi | |
17 | |
18 if [ $use_paired == 'Y' ] | |
19 then | |
20 options="$options -n -a -s ${fastq_file1}" | |
21 ${convert} ${options} ${srf_file} | |
22 #after conversion rename files | |
23 mv ${fastq_file1}_1.fastq ${fastq_file1} | |
24 mv ${fastq_file1}_2.fastq ${fastq_file2} | |
25 else | |
26 ${convert} ${options} ${srf_file} > ${fastq_file1} | |
27 fi | |
28 |