Commit 2aba8a3919ab254fceb0f94a577703df70fb7a11 - fastx-toolkit

Barcode-Splitter: uses Galaxy's output.files_path to store multiple output files. No need for a web public folder and URL tweaking anymore. A. Gordon 14 years ago

5 changed file(s) with 82 addition(s) and 80 deletion(s). Raw diff Collapse all Expand all

-1

galaxy/tools/fastx_toolkit/Makefile.am less more

15	15	fastx_clipper.xml \
16	16	fastx_reverse_complement.xml \
17	17	fastx_trimmer.xml \
18		fastx_barcode_splitter.xml \
	18	fastx_barcode_splitter.xml fastx_barcode_splitter_galaxy_wrapper.sh \
19	19	fastx_nucleotides_distribution.xml \
20	20	fastq_quality_boxplot.xml \
21	21	fasta_clipping_histogram.xml \

-1

galaxy/tools/fastx_toolkit/fastx_barcode_splitter.xml less more

0	0	<tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter">
1	1	<description></description>
2		<command>fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" --mismatches $mismatches --partial $partial $EOL > $output </command>
	2	<command interpreter="sh">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command>
3	3
4	4	<inputs>
5	5	<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />

+80

-0

galaxy/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh less more

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

-2

scripts/Makefile.am less more

8	8	# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
9	9
10	10	bin_SCRIPTS = fastx_barcode_splitter.pl \
11		fastx_barcode_splitter_galaxy_wrapper.sh \
12	11	fastx_nucleotide_distribution_graph.sh \
13	12	fastq_quality_boxplot_graph.sh \
14	13	fasta_clipping_histogram.pl
15	14
16	15	EXTRA_DIST = fastx_barcode_splitter.pl \
17		fastx_barcode_splitter_galaxy_wrapper.sh \
18	16	fastx_nucleotide_distribution_graph.sh \
19	17	fastq_quality_boxplot_graph.sh \
20	18	fasta_clipping_histogram.pl

-76

~~scripts/fastx_barcode_splitter_galaxy_wrapper.sh~~ less more

0		#!/bin/sh
1
2		# FASTX-toolkit - FASTA/FASTQ preprocessing tools.
3		# Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
4		#
5		# This program is free software: you can redistribute it and/or modify
6		# it under the terms of the GNU Affero General Public License as
7		# published by the Free Software Foundation, either version 3 of the
8		# License, or (at your option) any later version.
9		#
10		# This program is distributed in the hope that it will be useful,
11		# but WITHOUT ANY WARRANTY; without even the implied warranty of
12		# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13		# GNU Affero General Public License for more details.
14		#
15		# You should have received a copy of the GNU Affero General Public License
16		# along with this program. If not, see <http://www.gnu.org/licenses/>.
17
18		#
19		#This is a shell script wrapper for 'fastx_barcode_splitter.pl'
20		#
21		# 1. Output files are saved at a predefined location
22		# (Which was made publicly accessible using apache)
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 thier files)
27
28		BASEPATH="/media/sdb1/galaxy/barcode_splits/"
29		PUBLICURL="http://tango.cshl.edu/barcode_splits/"
30
31		BARCODE_FILE="$1"
32		FASTQ_FILE="$2"
33		LIBNAME="$3"
34		shift 3
35		# The rest of the parameters are passed to the split program
36
37		if [ "$LIBNAME" == "" ]; then
38		echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME]" >&2
39		exit 1
40		fi
41
42		#Sanitize library name, make sure we can create a file with this name
43		LIBNAME=${LIBNAME//\.gz/}
44		LIBNAME=${LIBNAME//\.txt/}
45		LIBNAME=${LIBNAME//[^[:alnum:]]/_}
46
47		if [ ! -r "$FASTQ_FILE" ]; then
48		echo "Error: Input file ($FASTQ_FILE) not found!" >&2
49		exit 1
50		fi
51		if [ ! -r "$BARCODE_FILE" ]; then
52		echo "Error: barcode file ($BARCODE_FILE) not found!" >&2
53		exit 1
54		fi
55
56		PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__"
57		SUFFIX=".txt"
58
59		RESULTS=`zcat -f "$FASTQ_FILE" \| fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"`
60		if [ $? != 0 ]; then
61		echo "error"
62		fi
63
64		#
65		# Convert the textual tab-separated table into simple HTML table,
66		# with the local path replaces with a valid URL
67		echo "<html><body><table border=1>"
68		echo "$RESULTS" \| sed "s\|$BASEPATH\|$PUBLICURL\|" \| sed '
69		i<tr><td>
70		s\|\t\|</td><td>\|g
71		s\|http.*\|<a href="&">&<\/a>\|
72		a<\/td><\/tr>
73		'
74		echo "<p><b>Copy these files to your local computer, as they will be soon deleted.</b>"
75		echo "</table></body></html>"