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author rnateam
date Thu, 17 Sep 2015 06:06:18 -0400
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="flexbar" version="2.4">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions os="linux" architecture="x86_64">
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7 <action type="download_by_url" target_filename="flexbar_v2.4_linux64.tgz">http://sourceforge.net/projects/flexbar/files/2.4/flexbar_v2.4_linux64.tgz</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
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12 </actions>
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13 <action type="set_environment">
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14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
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15 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
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16 </action>
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17 </actions_group>
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18 </install>
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19 <readme>
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20 Program: flexbar - flexible barcode and adapter removal
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21 Version: 2.4
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22
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23 SYNOPSIS
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24 flexbar -r reads [-t target] [-b barcodes] [-a adapters] [options]
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25
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26 DESCRIPTION
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27 -h, --help
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28 Displays this help message.
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29 -w, --advanced
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30 Print advanced options help screen.
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31 -i, --cite
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32 Show program reference for citation.
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33
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34 Basic options:
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35 -n, --threads NUM
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36 Number of threads to employ. Default: 1.
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37 -t, --target STR
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38 Prefix for output file names or paths. Default: flexbar.
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39 -r, --reads FILE
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40 Fasta/q file or stdin (-) with reads that may contain barcodes.
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41 -p, --reads2 FILE
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42 Second input file of paired reads, gz and bz2 files supported.
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43 -f, --format STR
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44 Quality format: sanger, solexa, i1.3, i1.5, i1.8 (illumina 1.8+).
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45 -c, --color-space
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46 Input in color-space format csfasta or csfastq in sanger scaling.
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47
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48 Barcode detection:
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49 -b, --barcodes FILE
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50 Fasta file with barcodes for demultiplexing that may contain N.
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51 -br, --barcode-reads FILE
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52 Fasta/q file composed of separate barcode reads for detection.
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53 -be, --barcode-trim-end STR
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54 Type of detection, see section trim-end modes. Default: ANY.
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55 -bo, --barcode-min-overlap NUM
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56 Minimum overlap of barcode and read. Default: barcode length.
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57 -bt, --barcode-threshold NUM
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58 Allowed mismatches and gaps per 10 bases overlap. Default: 1.0.
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59 -bu, --barcode-unassigned
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60 Include unassigned reads in output generation.
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61
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62 Adapter removal:
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63 -a, --adapters FILE
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64 Fasta file with adapters for removal that may contain N.
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65 -as, --adapter-seq STR
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66 Single adapter sequence as alternative to adapters option.
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67 -ae, --adapter-trim-end STR
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68 Type of removal, see section trim-end modes. Default: RIGHT.
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69 -ao, --adapter-min-overlap NUM
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70 Minimum overlap of adapter and read sequence. Default: 1.
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71 -at, --adapter-threshold NUM
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72 Allowed mismatches and gaps per 10 bases overlap. Default: 3.0.
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73
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74 Filtering and trimming:
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75 -u, --max-uncalled NUM
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76 Allowed uncalled bases (N or .) for each read. Default: 0.
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77 -x, --pre-trim-left NUM
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78 Trim given number of bases on 5' read end before detection.
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79 -y, --pre-trim-right NUM
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80 Trim specified number of bases on 3' end prior to detection.
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81 -q, --pre-trim-phred NUM
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82 Trim 3' end until specified or higher quality reached.
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83 -k, --post-trim-length NUM
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84 Trim to specified read length from 3' end after removal.
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85 -m, --min-read-length NUM
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86 Minimum read length to remain after removal. Default: 18.
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87
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88 Output selection:
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89 -o, --fasta-output
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90 Prefer non-quality formats fasta and csfasta for output.
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91 -z, --zip-output STR
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92 Enable direct compression of output files. One of GZ and BZ2.
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93 -s, --single-reads
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94 Write single paired reads for too short counterparts.
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95
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96 Logging and tagging:
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97 -l, --log-level STR
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98 Print valid optimal read alignment. One of ALL, MOD, and TAB.
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99 -g, --removal-tags
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100 Tag reads that are subject to adapter or barcode removal.
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101
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102 Trim-end modes:
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103 ANY: longer side of read remains after removal of overlap
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104 LEFT: right side remains after removal, align &lt;= read end
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105 RIGHT: left part remains after removal, align &gt;= read start
0
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106 LEFT_TAIL: consider first n bases of reads in alignment
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107 RIGHT_TAIL: use only last n bases, see tail-length options
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108
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109 EXAMPLES
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110 flexbar -r reads.fq -f i1.8 -t target -b brc.fa -a adap.fa
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111 flexbar -r reads.csfastq.gz -a adap.fa -ao 5 -ae LEFT -c
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112
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113 VERSION
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114 flexbar version: 2.4
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115 Last update July 29, 2013
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116
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117 Advanced options: flexbar -w
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118 </readme>
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119 </package>
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120 </tool_dependency>