/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh
Shell | 80 lines | 41 code | 9 blank | 30 comment | 7 complexity | 8a923b8288c6cffc061819f0defa6aad MD5 | raw file
1#!/bin/bash 2 3# FASTX-toolkit - FASTA/FASTQ preprocessing tools. 4# Copyright (C) 2009 A. Gordon (gordon@cshl.edu) 5# 6# This program is free software: you can redistribute it and/or modify 7# it under the terms of the GNU Affero General Public License as 8# published by the Free Software Foundation, either version 3 of the 9# License, or (at your option) any later version. 10# 11# This program is distributed in the hope that it will be useful, 12# but WITHOUT ANY WARRANTY; without even the implied warranty of 13# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 14# GNU Affero General Public License for more details. 15# 16# You should have received a copy of the GNU Affero General Public License 17# along with this program. If not, see <http://www.gnu.org/licenses/>. 18 19# 20#This is a shell script wrapper for 'fastx_barcode_splitter.pl' 21# 22# 1. Output files are saved at the dataset's files_path directory. 23# 24# 2. 'fastx_barcode_splitter.pl' outputs a textual table. 25# This script turns it into pretty HTML with working URL 26# (so lazy users can just click on the URLs and get their files) 27 28BARCODE_FILE="$1" 29FASTQ_FILE="$2" 30LIBNAME="$3" 31OUTPUT_PATH="$4" 32shift 4 33# The rest of the parameters are passed to the split program 34 35if [ "$OUTPUT_PATH" == "" ]; then 36 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 37 exit 1 38fi 39 40#Sanitize library name, make sure we can create a file with this name 41LIBNAME=${LIBNAME//\.gz/} 42LIBNAME=${LIBNAME//\.txt/} 43LIBNAME=${LIBNAME//[^[:alnum:]]/_} 44 45if [ ! -r "$FASTQ_FILE" ]; then 46 echo "Error: Input file ($FASTQ_FILE) not found!" >&2 47 exit 1 48fi 49if [ ! -r "$BARCODE_FILE" ]; then 50 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 51 exit 1 52fi 53mkdir -p "$OUTPUT_PATH" 54if [ ! -d "$OUTPUT_PATH" ]; then 55 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 56 exit 1 57fi 58 59PUBLICURL="" 60BASEPATH="$OUTPUT_PATH/" 61#PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" 62PREFIX="$BASEPATH""${LIBNAME}__" 63SUFFIX=".txt" 64 65RESULTS=`zcat -f "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` 66if [ $? != 0 ]; then 67 echo "error" 68fi 69 70# 71# Convert the textual tab-separated table into simple HTML table, 72# with the local path replaces with a valid URL 73echo "<html><body><table border=1>" 74echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|<a href=\"\\1\">\\1</a>|" | sed ' 75i<tr><td> 76s|\t|</td><td>|g 77a<\/td><\/tr> 78' 79echo "<p>" 80echo "</table></body></html>"