fastx_barcode_splitter_enhanced: fastx_barcode_splitter_galaxy

annotate fastx_barcode_splitter_galaxy_wrapper.sh @ 3:e7b7cdc1834d draft

planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit a3b5b09c69f880529df96bdd5e050d712fa35cf4-dirty

author	lparsons
date	Fri, 11 Mar 2016 17:24:31 -0500
parents	32304398ef67
children	0fb7e9130a70

rev	line source
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	1 #!/bin/bash
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	2
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	3 # FASTX-toolkit - FASTA/FASTQ preprocessing tools.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	4 # Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	5 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	6 # This program is free software: you can redistribute it and/or modify
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	7 # it under the terms of the GNU Affero General Public License as
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	8 # published by the Free Software Foundation, either version 3 of the
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	9 # License, or (at your option) any later version.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	10 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	11 # This program is distributed in the hope that it will be useful,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	14 # GNU Affero General Public License for more details.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	15 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	16 # You should have received a copy of the GNU Affero General Public License
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	17 # along with this program. If not, see <http://www.gnu.org/licenses/>.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	18
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	19 # Modified by Lance Parsons (lparsons@princeton.edu)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	20 # 2011-03-15 Adapted to allow galaxy to determine filetype
1 b7b3d008e2d3 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd lparsons parents: 0 diff changeset	21 # 2015-10-21 Updated to make compatible with OSX (BSD sed)
2 32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	22 # 2015-11-13 Removed LIBRARY_NAME, no longer needed
32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	23
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	24 #This is a shell script wrapper for 'fastx_barcode_splitter.pl'
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	25 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	26 # 1. Output files are saved at the dataset's files_path directory.
1 b7b3d008e2d3 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd lparsons parents: 0 diff changeset	27 #
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	28 # 2. 'fastx_barcode_splitter.pl' outputs a textual table.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	29 # This script turns it into pretty HTML with working URL
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	30 # (so lazy users can just click on the URLs and get their files)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	31
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	32 if [ "$1x" = "x" ]; then
2 32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	33 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	34 exit 1
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	35 fi
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	36
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	37 BARCODE_FILE="$1"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	38 FASTQ_FILE="$2"
2 32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	39 OUTPUT_PATH="$3"
32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	40 FILETYPE="$4"
32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	41 shift 4
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	42 # The rest of the parameters are passed to the split program
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	43
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	44 if [ "${OUTPUT_PATH}x" = "x" ]; then
2 32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	45 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	46 exit 1
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	47 fi
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	48
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	49 if [ ! -r "$FASTQ_FILE" ]; then
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	50 echo "Error: Input file ($FASTQ_FILE) not found!" >&2
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	51 exit 1
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	52 fi
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	53 if [ ! -r "$BARCODE_FILE" ]; then
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	54 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	55 exit 1
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	56 fi
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	57 mkdir -p "$OUTPUT_PATH"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	58 if [ ! -d "$OUTPUT_PATH" ]; then
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	59 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	60 exit 1
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	61 fi
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	62
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	63 BASEPATH="$OUTPUT_PATH/"
2 32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	64 PREFIX="$BASEPATH"
32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	65 SUFFIX=".$FILETYPE"
32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	66 DIRECTORY="$(cd "$(dirname "$0")" && pwd)"
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	67
2 32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	68 RESULTS=$(gzip -cdf "$FASTQ_FILE" \| "$DIRECTORY/fastx_barcode_splitter.pl" --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@")
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	69 if [ $? != 0 ]; then
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	70 echo "error"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	71 fi
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	72
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	73 #
2 32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	74 # Convert the textual tab-separated table into simple HTML table
1 b7b3d008e2d3 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd lparsons parents: 0 diff changeset	75 echo "<html><body><table border=1>"
2 32304398ef67 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4 lparsons parents: 1 diff changeset	76 echo "$RESULTS" \| sed "s\|$BASEPATH\$.*\$\|\\1\|" \| \
1 b7b3d008e2d3 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd lparsons parents: 0 diff changeset	77 perl -n -e '$_ =~ s\|\t\|</td><td>\|g; print "<tr><td>\n$_</td></tr>\n"'
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	78 echo "<p>"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	79 echo "</table></body></html>"

Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

annotate fastx_barcode_splitter_galaxy_wrapper.sh @ 3:e7b7cdc1834d draft