Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

annotate fastx_barcode_splitter_galaxy_wrapper.sh @ 1:b7b3d008e2d3 draft

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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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1 #!/bin/bash
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2
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3 # FASTX-toolkit - FASTA/FASTQ preprocessing tools.
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4 # Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
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5 #
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6 # This program is free software: you can redistribute it and/or modify
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7 # it under the terms of the GNU Affero General Public License as
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8 # published by the Free Software Foundation, either version 3 of the
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9 # License, or (at your option) any later version.
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10 #
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11 # This program is distributed in the hope that it will be useful,
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12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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14 # GNU Affero General Public License for more details.
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15 #
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16 # You should have received a copy of the GNU Affero General Public License
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17 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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18
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19 # Modified by Lance Parsons (lparsons@princeton.edu)
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20 # 2011-03-15 Adapted to allow galaxy to determine filetype
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b7b3d008e2d3 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd
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21 # 2015-10-21 Updated to make compatible with OSX (BSD sed)
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22 #
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23 #This is a shell script wrapper for 'fastx_barcode_splitter.pl'
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24 #
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25 # 1. Output files are saved at the dataset's files_path directory.
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26 #
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27 # 2. 'fastx_barcode_splitter.pl' outputs a textual table.
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28 # This script turns it into pretty HTML with working URL
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29 # (so lazy users can just click on the URLs and get their files)
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30
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31 if [ "$1x" = "x" ]; then
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32 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2
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33 exit 1
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34 fi
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35
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36 BARCODE_FILE="$1"
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37 FASTQ_FILE="$2"
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38 LIBNAME="$3"
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39 OUTPUT_PATH="$4"
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40 FILETYPE="$5"
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41 shift 5
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42 # The rest of the parameters are passed to the split program
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43
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44 if [ "${OUTPUT_PATH}x" = "x" ]; then
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45 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2
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46 exit 1
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47 fi
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48
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49 #Sanitize library name, make sure we can create a file with this name
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50 LIBNAME=${LIBNAME%.gz}
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51 LIBNAME=${LIBNAME%.txt}
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52 LIBNAME=$(echo "$LIBNAME" | tr -cd '[:alnum:]_')
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53
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54 if [ ! -r "$FASTQ_FILE" ]; then
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55 echo "Error: Input file ($FASTQ_FILE) not found!" >&2
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56 exit 1
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57 fi
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58 if [ ! -r "$BARCODE_FILE" ]; then
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59 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2
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60 exit 1
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61 fi
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62 mkdir -p "$OUTPUT_PATH"
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63 if [ ! -d "$OUTPUT_PATH" ]; then
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64 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2
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65 exit 1
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66 fi
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67
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68 PUBLICURL=""
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69 BASEPATH="$OUTPUT_PATH/"
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70 #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__"
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71 PREFIX="$BASEPATH""${LIBNAME}_"
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72 SUFFIX="_visible.$FILETYPE"
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73 DIRECTORY=$(cd `dirname $0` && pwd)
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74
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75 RESULTS=`gzip -cdf "$FASTQ_FILE" | $DIRECTORY/fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"`
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76 if [ $? != 0 ]; then
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77 echo "error"
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78 fi
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79
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80 #
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81 # Convert the textual tab-separated table into simple HTML table,
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82 # with the local path replaces with a valid URL
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83 #HTMLSUMMARY=${PREFIX}stats_visible_html
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84 echo "<html><body><table border=1>"
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85 echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|<a href=\"\\1\">\\1</a>|" | \
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86 perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"'
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87 echo "<p>"
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88 echo "</table></body></html>"