Mercurial > repos > dawe > srf2fastq
view 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 |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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#!/bin/sh #change this if the path is different convert=/usr/local/bin/srf2fastq srf_file=$1 use_filter=$2 use_paired=$3 fastq_file1=$4 fastq_file2=$5 options='-c ' if [ $use_filter == 'Y' ] then options="$options -C" fi if [ $use_paired == 'Y' ] then options="$options -n -a -s ${fastq_file1}" ${convert} ${options} ${srf_file} #after conversion rename files mv ${fastq_file1}_1.fastq ${fastq_file1} mv ${fastq_file1}_2.fastq ${fastq_file2} else ${convert} ${options} ${srf_file} > ${fastq_file1} fi