Mercurial > repos > hepcat72 > barcode_splitter_multi
view barcode_splitter_multi/barcode_splitter_galaxy_wrapper.sh @ 1:e3f91eee8c75 draft
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author | hepcat72 |
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date | Mon, 29 Aug 2016 15:21:20 -0400 |
parents | 50df2d629d51 |
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#!/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 # 2015-10-21 Updated to make compatible with OSX (BSD sed) # 2015-11-13 Removed LIBRARY_NAME, no longer needed # 2016-04-28 Output summary as simple tabular output # This is a shell script wrapper for 'fastx_barcode_splitter.pl' # # 1. Output files are saved at the dataset's files_path directory. if [ "$1x" = "x" ]; then echo "Usage: $0 [OUTPUT_PATH] [OUTFILETYPE] [OPTIONS]" >&2 exit 1 fi OUTPUT_PATH="$1" FILETYPE="$2" shift 2 # The rest of the parameters are passed to the split program if [ "${OUTPUT_PATH}x" = "x" ]; then echo "Usage: $0 [OUTPUT_PATH] [OUTFILETYPE] [OPTIONS]" >&2 exit 1 fi mkdir -p "$OUTPUT_PATH" if [ ! -d "$OUTPUT_PATH" ]; then echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 exit 1 fi PREFIX="$OUTPUT_PATH/" SUFFIX=".$FILETYPE" DIRECTORY="$(cd "$(dirname "$0")" && pwd)" RESULTS=$("$DIRECTORY/barcode_splitter.py" --format "$FILETYPE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@") if [ $? != 0 ]; then echo "error" fi echo "$RESULTS"