Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

annotate fastx_barcode_splitter_galaxy_wrapper.sh @ 4:0fb7e9130a70 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 460463a5406419fe8e113467bdb8bd093d21e7c5
author lparsons
date Mon, 02 May 2016 17:04:32 -0400
parents 32304398ef67
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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0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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20 # 2011-03-15 Adapted to allow galaxy to determine filetype
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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21 # 2015-10-21 Updated to make compatible with OSX (BSD sed)
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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22 # 2015-11-13 Removed LIBRARY_NAME, no longer needed
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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23 # 2016-04-28 Output summary as simple tabular output
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24
4
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25 # This is a shell script wrapper for 'fastx_barcode_splitter.pl'
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26 #
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27 # 1. Output files are saved at the dataset's files_path directory.
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28
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29 if [ "$1x" = "x" ]; then
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30 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
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31 exit 1
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32 fi
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33
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34 BARCODE_FILE="$1"
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35 FASTQ_FILE="$2"
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36 OUTPUT_PATH="$3"
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37 FILETYPE="$4"
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38 shift 4
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39 # The rest of the parameters are passed to the split program
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40
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41 if [ "${OUTPUT_PATH}x" = "x" ]; then
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42 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
0fb7e9130a70 planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit 460463a5406419fe8e113467bdb8bd093d21e7c5
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43 exit 1
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44 fi
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45
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46 if [ ! -r "$FASTQ_FILE" ]; then
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47 echo "Error: Input file ($FASTQ_FILE) not found!" >&2
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48 exit 1
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49 fi
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50 if [ ! -r "$BARCODE_FILE" ]; then
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51 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2
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52 exit 1
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53 fi
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54 mkdir -p "$OUTPUT_PATH"
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55 if [ ! -d "$OUTPUT_PATH" ]; then
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56 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2
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57 exit 1
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58 fi
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59
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60 BASEPATH="$OUTPUT_PATH/"
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61 PREFIX="$BASEPATH"
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62 SUFFIX=".$FILETYPE"
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63 DIRECTORY="$(cd "$(dirname "$0")" && pwd)"
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64
2
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65 RESULTS=$(gzip -cdf "$FASTQ_FILE" | "$DIRECTORY/fastx_barcode_splitter.pl" --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@")
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66 if [ $? != 0 ]; then
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67 echo "error"
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68 fi
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69
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70 echo "$RESULTS"