Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

comparison fastx_barcode_splitter_galaxy_wrapper.sh @ 2:32304398ef67 draft

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planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit c3b0be52079831f6ae58ff64e42d8ff54ce501e4
author lparsons
date Fri, 13 Nov 2015 12:43:14 -0500
parents b7b3d008e2d3
children 0fb7e9130a70
comparison
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1:b7b3d008e2d3 2:32304398ef67
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 # 22 # 2015-11-13 Removed LIBRARY_NAME, no longer needed
23
23 #This is a shell script wrapper for 'fastx_barcode_splitter.pl' 24 #This is a shell script wrapper for 'fastx_barcode_splitter.pl'
24 # 25 #
25 # 1. Output files are saved at the dataset's files_path directory. 26 # 1. Output files are saved at the dataset's files_path directory.
26 # 27 #
27 # 2. 'fastx_barcode_splitter.pl' outputs a textual table. 28 # 2. 'fastx_barcode_splitter.pl' outputs a textual table.
28 # This script turns it into pretty HTML with working URL 29 # This script turns it into pretty HTML with working URL
29 # (so lazy users can just click on the URLs and get their files) 30 # (so lazy users can just click on the URLs and get their files)
30 31
31 if [ "$1x" = "x" ]; then 32 if [ "$1x" = "x" ]; then
32 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2 33 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
33 exit 1 34 exit 1
34 fi 35 fi
35 36
36 BARCODE_FILE="$1" 37 BARCODE_FILE="$1"
37 FASTQ_FILE="$2" 38 FASTQ_FILE="$2"
38 LIBNAME="$3" 39 OUTPUT_PATH="$3"
39 OUTPUT_PATH="$4" 40 FILETYPE="$4"
40 FILETYPE="$5" 41 shift 4
41 shift 5
42 # The rest of the parameters are passed to the split program 42 # The rest of the parameters are passed to the split program
43 43
44 if [ "${OUTPUT_PATH}x" = "x" ]; then 44 if [ "${OUTPUT_PATH}x" = "x" ]; then
45 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2 45 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
46 exit 1 46 exit 1
47 fi 47 fi
48
49 #Sanitize library name, make sure we can create a file with this name
50 LIBNAME=${LIBNAME%.gz}
51 LIBNAME=${LIBNAME%.txt}
52 LIBNAME=$(echo "$LIBNAME" | tr -cd '[:alnum:]_')
53 48
54 if [ ! -r "$FASTQ_FILE" ]; then 49 if [ ! -r "$FASTQ_FILE" ]; then
55 echo "Error: Input file ($FASTQ_FILE) not found!" >&2 50 echo "Error: Input file ($FASTQ_FILE) not found!" >&2
56 exit 1 51 exit 1
57 fi 52 fi
63 if [ ! -d "$OUTPUT_PATH" ]; then 58 if [ ! -d "$OUTPUT_PATH" ]; then
64 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 59 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2
65 exit 1 60 exit 1
66 fi 61 fi
67 62
68 PUBLICURL=""
69 BASEPATH="$OUTPUT_PATH/" 63 BASEPATH="$OUTPUT_PATH/"
70 #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" 64 PREFIX="$BASEPATH"
71 PREFIX="$BASEPATH""${LIBNAME}_" 65 SUFFIX=".$FILETYPE"
72 SUFFIX="_visible.$FILETYPE" 66 DIRECTORY="$(cd "$(dirname "$0")" && pwd)"
73 DIRECTORY=$(cd `dirname $0` && pwd)
74 67
75 RESULTS=`gzip -cdf "$FASTQ_FILE" | $DIRECTORY/fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` 68 RESULTS=$(gzip -cdf "$FASTQ_FILE" | "$DIRECTORY/fastx_barcode_splitter.pl" --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@")
76 if [ $? != 0 ]; then 69 if [ $? != 0 ]; then
77 echo "error" 70 echo "error"
78 fi 71 fi
79 72
80 # 73 #
81 # Convert the textual tab-separated table into simple HTML table, 74 # Convert the textual tab-separated table into simple HTML table
82 # with the local path replaces with a valid URL
83 #HTMLSUMMARY=${PREFIX}stats_visible_html
84 echo "<html><body><table border=1>" 75 echo "<html><body><table border=1>"
85 echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|<a href=\"\\1\">\\1</a>|" | \ 76 echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|\\1|" | \
86 perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"' 77 perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"'
87 echo "<p>" 78 echo "<p>"
88 echo "</table></body></html>" 79 echo "</table></body></html>"