Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced
diff fastx_barcode_splitter_galaxy_wrapper.sh @ 0:84bbf4fd24c3 draft
Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history.
| author | lparsons |
|---|---|
| date | Fri, 08 Nov 2013 09:53:39 -0500 |
| parents | |
| children | b7b3d008e2d3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_barcode_splitter_galaxy_wrapper.sh Fri Nov 08 09:53:39 2013 -0500 @@ -0,0 +1,90 @@ +#!/bin/bash + +# FASTX-toolkit - FASTA/FASTQ preprocessing tools. +# Copyright (C) 2009 A. Gordon (gordon@cshl.edu) +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + +# Modified by Lance Parsons (lparsons@princeton.edu) +# 2011-03-15 Adapted to allow galaxy to determine filetype +# +#This is a shell script wrapper for 'fastx_barcode_splitter.pl' +# +# 1. Output files are saved at the dataset's files_path directory. +# +# 2. 'fastx_barcode_splitter.pl' outputs a textual table. +# This script turns it into pretty HTML with working URL +# (so lazy users can just click on the URLs and get their files) + +if [ "$1x" = "x" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2 + exit 1 +fi + +BARCODE_FILE="$1" +FASTQ_FILE="$2" +LIBNAME="$3" +OUTPUT_PATH="$4" +FILETYPE="$5" +shift 5 +# The rest of the parameters are passed to the split program + +if [ "${OUTPUT_PATH}x" = "x" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2 + exit 1 +fi + +#Sanitize library name, make sure we can create a file with this name +LIBNAME=${LIBNAME%.gz} +LIBNAME=${LIBNAME%.txt} +LIBNAME=$(echo "$LIBNAME" | tr -cd '[:alnum:]_') + +if [ ! -r "$FASTQ_FILE" ]; then + echo "Error: Input file ($FASTQ_FILE) not found!" >&2 + exit 1 +fi +if [ ! -r "$BARCODE_FILE" ]; then + echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 + exit 1 +fi +mkdir -p "$OUTPUT_PATH" +if [ ! -d "$OUTPUT_PATH" ]; then + echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 + exit 1 +fi + +PUBLICURL="" +BASEPATH="$OUTPUT_PATH/" +#PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" +PREFIX="$BASEPATH""${LIBNAME}_" +SUFFIX="_visible_$FILETYPE" +DIRECTORY=$(cd `dirname $0` && pwd) + +RESULTS=`gzip -cdf "$FASTQ_FILE" | $DIRECTORY/fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` +if [ $? != 0 ]; then + echo "error" +fi + +# +# Convert the textual tab-separated table into simple HTML table, +# with the local path replaces with a valid URL +#HTMLSUMMARY=${PREFIX}stats_visible_html +echo "<html><body><table border=1>" +echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed ' +i<tr><td> +s|\t|</td><td>|g +a<\/td><\/tr> +' +echo "<p>" +echo "</table></body></html>"