Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

comparison fastx_barcode_splitter_galaxy_wrapper.sh @ 4:0fb7e9130a70 draft default tip

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
author lparsons
date Mon, 02 May 2016 17:04:32 -0400
parents 32304398ef67
children
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3:e7b7cdc1834d 4:0fb7e9130a70
15 # 15 #
16 # You should have received a copy of the GNU Affero General Public License 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/>. 17 # along with this program. If not, see <http://www.gnu.org/licenses/>.
18 18
19 # Modified by Lance Parsons (lparsons@princeton.edu) 19 # Modified by Lance Parsons (lparsons@princeton.edu)
20 # 2011-03-15 Adapted to allow galaxy to determine filetype 20 # 2011-03-15 Adapted to allow galaxy to determine filetype
21 # 2015-10-21 Updated to make compatible with OSX (BSD sed) 21 # 2015-10-21 Updated to make compatible with OSX (BSD sed)
22 # 2015-11-13 Removed LIBRARY_NAME, no longer needed 22 # 2015-11-13 Removed LIBRARY_NAME, no longer needed
23 # 2016-04-28 Output summary as simple tabular output
23 24
24 #This is a shell script wrapper for 'fastx_barcode_splitter.pl' 25 # This is a shell script wrapper for 'fastx_barcode_splitter.pl'
25 # 26 #
26 # 1. Output files are saved at the dataset's files_path directory. 27 # 1. Output files are saved at the dataset's files_path directory.
27 #
28 # 2. 'fastx_barcode_splitter.pl' outputs a textual table.
29 # This script turns it into pretty HTML with working URL
30 # (so lazy users can just click on the URLs and get their files)
31 28
32 if [ "$1x" = "x" ]; then 29 if [ "$1x" = "x" ]; then
33 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2 30 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
34 exit 1 31 exit 1
35 fi 32 fi
36 33
37 BARCODE_FILE="$1" 34 BARCODE_FILE="$1"
38 FASTQ_FILE="$2" 35 FASTQ_FILE="$2"
39 OUTPUT_PATH="$3" 36 OUTPUT_PATH="$3"
40 FILETYPE="$4" 37 FILETYPE="$4"
41 shift 4 38 shift 4
42 # The rest of the parameters are passed to the split program 39 # The rest of the parameters are passed to the split program
43 40
44 if [ "${OUTPUT_PATH}x" = "x" ]; then 41 if [ "${OUTPUT_PATH}x" = "x" ]; then
45 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2 42 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
46 exit 1 43 exit 1
47 fi 44 fi
48 45
49 if [ ! -r "$FASTQ_FILE" ]; then 46 if [ ! -r "$FASTQ_FILE" ]; then
50 echo "Error: Input file ($FASTQ_FILE) not found!" >&2 47 echo "Error: Input file ($FASTQ_FILE) not found!" >&2
51 exit 1 48 exit 1
52 fi 49 fi
53 if [ ! -r "$BARCODE_FILE" ]; then 50 if [ ! -r "$BARCODE_FILE" ]; then
54 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 51 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2
55 exit 1 52 exit 1
56 fi 53 fi
57 mkdir -p "$OUTPUT_PATH" 54 mkdir -p "$OUTPUT_PATH"
58 if [ ! -d "$OUTPUT_PATH" ]; then 55 if [ ! -d "$OUTPUT_PATH" ]; then
59 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 56 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2
60 exit 1 57 exit 1
61 fi 58 fi
62 59
63 BASEPATH="$OUTPUT_PATH/" 60 BASEPATH="$OUTPUT_PATH/"
64 PREFIX="$BASEPATH" 61 PREFIX="$BASEPATH"
65 SUFFIX=".$FILETYPE" 62 SUFFIX=".$FILETYPE"
66 DIRECTORY="$(cd "$(dirname "$0")" && pwd)" 63 DIRECTORY="$(cd "$(dirname "$0")" && pwd)"
67 64
68 RESULTS=$(gzip -cdf "$FASTQ_FILE" | "$DIRECTORY/fastx_barcode_splitter.pl" --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@") 65 RESULTS=$(gzip -cdf "$FASTQ_FILE" | "$DIRECTORY/fastx_barcode_splitter.pl" --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@")
69 if [ $? != 0 ]; then 66 if [ $? != 0 ]; then
70 echo "error" 67 echo "error"
71 fi 68 fi
72 69
73 # 70 echo "$RESULTS"
74 # Convert the textual tab-separated table into simple HTML table
75 echo "<html><body><table border=1>"
76 echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|\\1|" | \
77 perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"'
78 echo "<p>"
79 echo "</table></body></html>"