Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced
diff fastx_barcode_splitter_galaxy_wrapper.sh @ 1:b7b3d008e2d3 draft
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd
| author | lparsons |
|---|---|
| date | Tue, 27 Oct 2015 11:47:52 -0400 |
| parents | 84bbf4fd24c3 |
| children | 32304398ef67 |
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--- a/fastx_barcode_splitter_galaxy_wrapper.sh Fri Nov 08 09:53:39 2013 -0500 +++ b/fastx_barcode_splitter_galaxy_wrapper.sh Tue Oct 27 11:47:52 2015 -0400 @@ -18,11 +18,12 @@ # 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) # #This is a shell script wrapper for 'fastx_barcode_splitter.pl' # # 1. Output files are saved at the dataset's files_path directory. -# +# # 2. 'fastx_barcode_splitter.pl' outputs a textual table. # This script turns it into pretty HTML with working URL # (so lazy users can just click on the URLs and get their files) @@ -68,7 +69,7 @@ BASEPATH="$OUTPUT_PATH/" #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" PREFIX="$BASEPATH""${LIBNAME}_" -SUFFIX="_visible_$FILETYPE" +SUFFIX="_visible.$FILETYPE" DIRECTORY=$(cd `dirname $0` && pwd) RESULTS=`gzip -cdf "$FASTQ_FILE" | $DIRECTORY/fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` @@ -80,11 +81,8 @@ # Convert the textual tab-separated table into simple HTML table, # with the local path replaces with a valid URL #HTMLSUMMARY=${PREFIX}stats_visible_html -echo "<html><body><table border=1>" -echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed ' -i<tr><td> -s|\t|</td><td>|g -a<\/td><\/tr> -' +echo "<html><body><table border=1>" +echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|<a href=\"\\1\">\\1</a>|" | \ +perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"' echo "<p>" echo "</table></body></html>"