Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced
diff fastx_barcode_splitter_galaxy_wrapper.sh @ 2:32304398ef67 draft
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 |
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--- a/fastx_barcode_splitter_galaxy_wrapper.sh Tue Oct 27 11:47:52 2015 -0400 +++ b/fastx_barcode_splitter_galaxy_wrapper.sh Fri Nov 13 12:43:14 2015 -0500 @@ -19,7 +19,8 @@ # 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 + #This is a shell script wrapper for 'fastx_barcode_splitter.pl' # # 1. Output files are saved at the dataset's files_path directory. @@ -29,28 +30,22 @@ # (so lazy users can just click on the URLs and get their files) if [ "$1x" = "x" ]; then - echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2 + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2 exit 1 fi BARCODE_FILE="$1" FASTQ_FILE="$2" -LIBNAME="$3" -OUTPUT_PATH="$4" -FILETYPE="$5" -shift 5 +OUTPUT_PATH="$3" +FILETYPE="$4" +shift 4 # The rest of the parameters are passed to the split program if [ "${OUTPUT_PATH}x" = "x" ]; then - echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2 + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2 exit 1 fi -#Sanitize library name, make sure we can create a file with this name -LIBNAME=${LIBNAME%.gz} -LIBNAME=${LIBNAME%.txt} -LIBNAME=$(echo "$LIBNAME" | tr -cd '[:alnum:]_') - if [ ! -r "$FASTQ_FILE" ]; then echo "Error: Input file ($FASTQ_FILE) not found!" >&2 exit 1 @@ -65,24 +60,20 @@ exit 1 fi -PUBLICURL="" BASEPATH="$OUTPUT_PATH/" -#PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" -PREFIX="$BASEPATH""${LIBNAME}_" -SUFFIX="_visible.$FILETYPE" -DIRECTORY=$(cd `dirname $0` && pwd) +PREFIX="$BASEPATH" +SUFFIX=".$FILETYPE" +DIRECTORY="$(cd "$(dirname "$0")" && pwd)" -RESULTS=`gzip -cdf "$FASTQ_FILE" | $DIRECTORY/fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` +RESULTS=$(gzip -cdf "$FASTQ_FILE" | "$DIRECTORY/fastx_barcode_splitter.pl" --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@") if [ $? != 0 ]; then echo "error" fi # -# Convert the textual tab-separated table into simple HTML table, -# with the local path replaces with a valid URL -#HTMLSUMMARY=${PREFIX}stats_visible_html +# Convert the textual tab-separated table into simple HTML table echo "<html><body><table border=1>" -echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|<a href=\"\\1\">\\1</a>|" | \ +echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|\\1|" | \ perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"' echo "<p>" echo "</table></body></html>"