Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

annotate fastx_barcode_splitter_galaxy_wrapper.sh @ 7:06ebd94d80ae 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 c3b0be52079831f6ae58ff64e42d8ff54ce501e4
author lparsons
date Fri, 13 Nov 2015 12:42:49 -0500
parents 51e098891465
children
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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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21 # 2015-10-21 Updated to make compatible with OSX (BSD sed)
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22 # 2015-11-13 Removed LIBRARY_NAME, no longer needed
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23
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24 #This is a shell script wrapper for 'fastx_barcode_splitter.pl'
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25 #
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26 # 1. Output files are saved at the dataset's files_path directory.
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27 #
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28 # 2. 'fastx_barcode_splitter.pl' outputs a textual table.
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29 # This script turns it into pretty HTML with working URL
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30 # (so lazy users can just click on the URLs and get their files)
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32 if [ "$1x" = "x" ]; then
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33 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
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34 exit 1
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35 fi
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36
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37 BARCODE_FILE="$1"
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38 FASTQ_FILE="$2"
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39 OUTPUT_PATH="$3"
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40 FILETYPE="$4"
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41 shift 4
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42 # The rest of the parameters are passed to the split program
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43
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44 if [ "${OUTPUT_PATH}x" = "x" ]; then
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45 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
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46 exit 1
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47 fi
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48
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49 if [ ! -r "$FASTQ_FILE" ]; then
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50 echo "Error: Input file ($FASTQ_FILE) not found!" >&2
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51 exit 1
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52 fi
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53 if [ ! -r "$BARCODE_FILE" ]; then
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54 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2
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55 exit 1
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56 fi
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57 mkdir -p "$OUTPUT_PATH"
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58 if [ ! -d "$OUTPUT_PATH" ]; then
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59 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2
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60 exit 1
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61 fi
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63 BASEPATH="$OUTPUT_PATH/"
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64 PREFIX="$BASEPATH"
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65 SUFFIX=".$FILETYPE"
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66 DIRECTORY="$(cd "$(dirname "$0")" && pwd)"
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67
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68 RESULTS=$(gzip -cdf "$FASTQ_FILE" | "$DIRECTORY/fastx_barcode_splitter.pl" --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@")
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69 if [ $? != 0 ]; then
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70 echo "error"
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71 fi
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73 #
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74 # Convert the textual tab-separated table into simple HTML table
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75 echo "<html><body><table border=1>"
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76 echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|\\1|" | \
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77 perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"'
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78 echo "<p>"
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79 echo "</table></body></html>"