Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 21:e798c0b3384c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
author iuc
date Tue, 10 Apr 2018 18:39:49 -0400
parents fcc6efc4ef6d
children b2f8e8b8b9a3
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fcc6efc4ef6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340
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1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.1" profile="17.01">
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2 <description>- map reads against reference genome</description>
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3 <macros>
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4 <import>bowtie2_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.3.4">bowtie2</requirement>
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8 <requirement type="package" version="1.6">samtools</requirement>
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9 </requirements>
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10 <version_command>bowtie2 --version</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 ## Use pipefail if available to quit with first non-zero exit code
e798c0b3384c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c
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13 set -o | grep -q pipefail && set -o pipefail;
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14 ## prepare bowtie2 index
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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15 #set index_path = ''
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16 #if str($reference_genome.source) == "history":
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17 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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18 ln -s -f '$reference_genome.own_file' genome.fa &&
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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19 #set index_path = 'genome'
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20 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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21 #set index_path = $reference_genome.index.fields.path
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22 #end if
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24 ## Link in the input files, so bowtie2 can tell their type
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26 #set compressed="False"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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27 #set reads_are_fastq = True
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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28 #if str($library.type) == 'paired':
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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29 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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30 #set read1 = "input_f.fastq.gz"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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31 #set compressed = "GZ"
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32 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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33 #set read1 = "input_f.fastq.bz2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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34 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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35 #else if $library.input_1.is_of_type('fasta'):
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36 #set reads_are_fastq = False
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37 #set read1 = "input_f.fasta"
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38 #else:
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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39 #set read1 = "input_f.fastq"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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40 #end if
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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41 ln -f -s '${library.input_1}' ${read1} &&
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43 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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44 #set read2 = "input_r.fastq.gz"
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45 #set compressed = "GZ"
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46 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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47 #set read2 = "input_r.fastq.bz2"
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48 #set compressed = "BZ2"
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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49 #else if $library.input_2.is_of_type('fasta'):
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50 #set read2 = "input_r.fasta"
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51 #else:
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52 #set read2 = "input_r.fastq"
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53 #end if
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54 ln -f -s '${library.input_2}' ${read2} &&
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55 #else if str($library.type) == 'paired_collection':
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56 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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57 #set read1 = "input_f.fastq.gz"
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58 #set compressed = "GZ"
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59 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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60 #set read1 = "input_f.fastq.bz2"
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61 #set compressed = "BZ2"
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62 #else if $library.input_1.forward.is_of_type('fasta'):
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63 #set reads_are_fastq = False
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64 #set read1 = "input_f.fasta"
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65 #else:
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66 #set read1 = "input_f.fastq"
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67 #end if
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68 ln -s '${library.input_1.forward}' ${read1} &&
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69
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70 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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71 #set read2 = "input_r.fastq.gz"
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72 #set compressed = "GZ"
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73 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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74 #set read2 = "input_r.fastq.bz2"
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75 #set compressed = "BZ2"
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76 #else if $library.input_1.reverse.is_of_type("fasta"):
e0ca9500999b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit a887e11c533af3ed3734c26da2da33aa8acbbce9
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77 #set read2 = "input_r.fasta"
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78 #else:
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79 #set read2 = "input_r.fastq"
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80 #end if
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81 ln -s '${library.input_1.reverse}' ${read2} &&
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82
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83 #else if str($library.type) == 'paired_interleaved':
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84 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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85 #set read1 = "input_il.fastq.gz"
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86 #set compressed = "GZ"
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87 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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88 #set read1 = "input_il.fastq.bz2"
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89 #set compressed = "BZ2"
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90 #else if $library.input_1.is_of_type("fasta"):
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91 #set reads_are_fastq = False
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92 #set read1 = "input_il.fasta"
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93 #else:
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94 #set read1 = "input_il.fastq"
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95 #end if
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96 ln -s '${library.input_1}' ${read1} &&
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97 #else:
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98 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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99 #set read1 = "input_f.fastq.gz"
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100 #set compressed = "GZ"
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101 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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102 #set read1 = "input_f.fastq.bz2"
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103 #set compressed = "BZ2"
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104 #else if $library.input_1.is_of_type("fasta"):
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105 #set reads_are_fastq = False
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106 #set read1 = "input_f.fasta"
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107 #else:
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108 #set read1 = "input_f.fastq"
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109 #end if
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110 ln -s '${library.input_1}' ${read1} &&
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111 #end if
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112
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113 ## execute bowtie2
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114
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115 bowtie2
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116
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117 ## number of threads
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118 -p \${GALAXY_SLOTS:-4}
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119
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120 ## index file path
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121 -x '$index_path'
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122
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123 ## Input reads are fasta?
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124 #if not reads_are_fastq:
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125 -f
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126 #end if
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127
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128 ## Input reads
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129 #if str( $library.type ) == "single":
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130 -U '${read1}'
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131 #if str( $library.unaligned_file ) == "true":
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132 #if $compressed == "GZ":
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133 --un-gz '${output_unaligned_reads_l}'
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134 #else if $compressed == "BZ2":
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135 --un-bz2 '${output_unaligned_reads_l}'
14
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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136 #else:
18
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137 --un '${output_unaligned_reads_l}'
14
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138 #end if
18
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139 #end if
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140 #if str( $library.aligned_file ) == "true":
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141 #if $compressed == "GZ":
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142 --al-gz '${output_aligned_reads_l}'
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143 #else if $compressed == "BZ2":
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144 --al-bz2 '${output_aligned_reads_l}'
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145 #else:
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146 --al '${output_aligned_reads_l}'
16
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147 #end if
18
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148 #end if
15
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149
18
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150 #elif str( $library.type ) == "paired_interleaved":
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151 --interleaved '${read1}'
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152 #if str( $library.unaligned_file ) == "true":
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153 #if $compressed == "GZ":
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154 --un-gz '${output_unaligned_reads_l}'
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155 #else if $compressed == "BZ2":
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156 --un-bz2 '${output_unaligned_reads_l}'
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157 #else:
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158 --un '${output_unaligned_reads_l}'
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159 #end if
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160 #end if
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161 #if str( $library.aligned_file ) == "true":
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162 #if $compressed == "GZ":
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163 --al-gz '${output_aligned_reads_l}'
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164 #else if $compressed == "BZ2":
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165 --al-bz2 '${output_aligned_reads_l}'
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166 #else:
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167 --al '${output_aligned_reads_l}'
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168 #end if
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169 #end if
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170 #else:
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171 -1 '${read1}'
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172 -2 '${read2}'
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173 #if str( $library.unaligned_file ) == "true":
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174 #if $compressed == "GZ":
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175 --un-conc-gz '${output_unaligned_reads_l}'
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176 #else if $compressed == "BZ2":
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177 --un-conc-bz2 '${output_unaligned_reads_l}'
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178 #else:
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179 --un-conc '${output_unaligned_reads_l}'
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180 #end if
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181 #end if
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182 #if str( $library.aligned_file ) == "true":
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183 #if $compressed == "GZ":
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184 --al-conc-gz '${output_aligned_reads_l}'
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185 #else if $compressed == "BZ2":
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186 --al-conc-bz2 '${output_aligned_reads_l}'
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187 #else:
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188 --al-conc '${output_aligned_reads_l}'
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189 #end if
18
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190 #end if
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191 #if str( $library.paired_options.paired_options_selector ) == "yes":
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192 -I ${library.paired_options.I}
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193 -X ${library.paired_options.X}
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194 ${library.paired_options.fr_rf_ff}
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195 ${library.paired_options.no_mixed}
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196 ${library.paired_options.no_discordant}
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197 ${library.paired_options.dovetail}
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198 ${library.paired_options.no_contain}
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199 ${library.paired_options.no_overlap}
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200 #end if
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201 #end if
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202
18
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203 ## Read group information.
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204 @define_read_group_helpers@
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205 #if str( $library.type ) == "single":
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206 #set $rg_auto_name = $read_group_name_default($library.input_1)
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207 #elif str( $library.type ) == "paired":
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208 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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209 #else
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210 #set $rg_auto_name = $read_group_name_default($library.input_1)
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211 #end if
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212 @set_use_rg_var@
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213 @set_read_group_vars@
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214 #if $use_rg
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215 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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216 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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217 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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218 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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219 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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220 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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221 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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222 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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223 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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224 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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225 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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226 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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227 #end if
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228
18
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229 ## Analysis type
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230 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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231 $analysis_type.presets
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232 #elif str( $analysis_type.analysis_type_selector ) == "full":
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233 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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234 --skip ${analysis_type.input_options.skip}
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235 --qupto ${analysis_type.input_options.qupto}
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236 --trim5 ${analysis_type.input_options.trim5}
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237 --trim3 ${analysis_type.input_options.trim3}
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238 ${analysis_type.input_options.qv_encoding}
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239 ${analysis_type.input_options.solexa_quals}
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240 ${analysis_type.input_options.int_quals}
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241 #end if
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242
18
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243 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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244 -N ${analysis_type.alignment_options.N}
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245 -L ${analysis_type.alignment_options.L}
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246 -i '${analysis_type.alignment_options.i}'
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247 --n-ceil '${analysis_type.alignment_options.n_ceil}'
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248 --dpad ${analysis_type.alignment_options.dpad}
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249 --gbar ${analysis_type.alignment_options.gbar}
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250 ${analysis_type.alignment_options.ignore_quals}
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251 ${analysis_type.alignment_options.nofw}
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252 ${analysis_type.alignment_options.norc}
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253 ${analysis_type.alignment_options.no_1mm_upfront}
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254 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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255 --end-to-end
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256 --score-min '${analysis_type.alignment_options.align_mode.score_min_ete}'
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257 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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258 --local
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259 --score-min '${analysis_type.alignment_options.align_mode.score_min_loc}'
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260 #end if
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261 #end if
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262
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263 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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264 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
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265 --ma ${analysis_type.scoring_options.ma}
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266 #end if
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267 --mp '${analysis_type.scoring_options.mp}'
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268 --np ${analysis_type.scoring_options.np}
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269 --rdg ${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}
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270 --rfg ${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}
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271 #end if
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272
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273 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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274 -k ${analysis_type.reporting_options.k}
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275 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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276 -a
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277 #end if
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278
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279 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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280 -D ${analysis_type.effort_options.D}
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281 -R ${analysis_type.effort_options.R}
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282 #end if
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283
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284 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
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285 ${analysis_type.sam_options.no_unal}
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286 ${analysis_type.sam_options.omit_sec_seq}
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287 ${analysis_type.sam_options.sam_no_qname_trunc}
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288 ${analysis_type.sam_options.xeq}
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289 ${analysis_type.sam_options.soft_clipped_unmapped_tlen}
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290 #end if
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291
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292 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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293 ${analysis_type.other_options.reorder}
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294 ${analysis_type.other_options.non_deterministic}
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295 --seed ${analysis_type.other_options.seed}
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296 #end if
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297
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298 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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299 ${analysis_type.cline}
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300 #end if
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301
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302 ## mapping stats (i.e. stderr from bowtie2)
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303 #if $save_mapping_stats
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304 2> '$mapping_stats'
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305 #end if
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306
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307 ## output file
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308 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
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309 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$output'
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310 #else
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311 > '$output_sam'
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312 #end if
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313
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314 ## rename unaligned sequence files
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315 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
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316 #from os.path import splitext
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317 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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318 && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
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319 && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
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320 #end if
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321 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
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322 #from os.path import splitext
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323 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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324 && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
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325 && mv '${ _aligned_root }.2${_aligned_ext}' '$output_aligned_reads_r'
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326 #end if
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327
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328 ]]></command>
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329 <inputs>
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330 <!-- single/paired -->
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331 <conditional name="library">
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332 <param name="type" type="select" label="Is this single or paired library">
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333 <option value="single">Single-end</option>
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334 <option value="paired">Paired-end</option>
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335 <option value="paired_collection">Paired-end Dataset Collection</option>
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336 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
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337 </param>
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338
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339 <when value="single">
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340 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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341 <expand macro="align_unalign" />
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342 </when>
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343 <when value="paired">
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344 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #1" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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345 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTA/Q file #2" help="Must be of datatype &quot;fastqsanger&quot;or &quot;fasta&quot;" />
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346 <expand macro="align_unalign" />
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347 <expand macro="paired_end_options" />
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348 </when>
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349 <when value="paired_collection">
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350 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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351 <expand macro="align_unalign" />
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352 <expand macro="paired_end_options" />
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353 </when>
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354 <when value="paired_interleaved">
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355 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="Interleaved FASTQ file" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;. --interleaved"/>
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356 <expand macro="align_unalign" />
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357 <expand macro="paired_end_options" />
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358 </when>
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359 </conditional>
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360 <!-- reference genome -->
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361 <conditional name="reference_genome">
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362 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
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363 <option value="indexed">Use a built-in genome index</option>
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364 <option value="history">Use a genome from the history and build index</option>
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365 </param>
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366 <when value="indexed">
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367 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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368 <options from_data_table="bowtie2_indexes">
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369 <filter type="sort_by" column="2"/>
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370 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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371 </options>
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372 </param>
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373 </when>
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374 <when value="history">
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375 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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376 </when>
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377 </conditional>
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378 <!-- read group settings -->
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379 <expand macro="read_group_conditional" />
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380 <conditional name="analysis_type">
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381 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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382 <option value="simple">1: Default setting only</option>
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383 <option value="full">2: Full parameter list</option>
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384 </param>
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385 <when value="simple">
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386 <param name="presets" type="select" display="radio" label="Do you want to use presets?" help="Allow selecting among several preset parameter settings. Choosing between these will result in dramatic changes in runtime. See help below to understand effects of these presets.">
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387 <option value="no_presets" selected="True">No, just use defaults</option>
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388 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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389 <option value="--fast">Fast end-to-end (--fast)</option>
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390 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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391 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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392 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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393 <option value="--fast-local">Fast local (--fast-local)</option>
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394 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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395 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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396 </param>
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397 </when>
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398 <when value="full">
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399 <conditional name="input_options">
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400 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See &quot;Input Options&quot; section of Help below for information">
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401 <option value="yes">Yes</option>
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402 <option value="no" selected="true">No</option>
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403 </param>
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404 <when value="yes">
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405 <param name="skip" type="integer" min="0" value="0" label="Skip (i.e. do not align) the first that many reads or pairs in the input" help="-s/--skip; default=0"/>
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406 <param name="qupto" type="integer" min="1" value="100000000" label="Align the first that many reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop" help="-u/--qupto; for default behavior (no limit) leave this value very large"/>
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407 <param name="trim5" type="integer" min="0" value="0" label="Trim that many bases from 5' (left) end of each read before alignment" help="-5/--trim5; default=0"/>
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408 <param name="trim3" type="integer" min="0" value="0" label="Trim that many bases from 3' (right) end of each read before alignment" help="-3/--trim3; default=0"/>
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409 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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410 <option value="--phred33" selected="True">Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines (--phred33)</option>
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411 <option value="--phred64">Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding (--phred64)</option>
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412 </param>
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413 <param name="solexa_quals" type="boolean" truevalue="--solexa-quals" falsevalue="" checked="False" label="Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3)" help="--solexa-quals; default=False"/>
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414 <param name="int_quals" type="boolean" truevalue="--int-quals" falsevalue="" checked="False" label="Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified" help="--int-quals; default=False"/>
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415 </when>
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416 <when value="no">
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417 <!-- do nothing -->
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418 </when>
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419 </conditional>
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420 <conditional name="alignment_options">
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421 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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422 <option value="yes">Yes</option>
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423 <option value="no" selected="true">No</option>
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424 </param>
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425 <when value="yes">
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426 <param name="N" type="integer" min="0" max="1" value="0" label="Set the number of mismatches to be allowed in a seed alignment during multiseed alignment (see `Multiseed alignment` section of help below)" help="-N; Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity; default=0"/>
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427 <param name="L" type="integer" min="0" max="32" value="22" label="Sets the length of the seed substrings to align during multiseed alignment (see `Multiseed alignment` section of help below)" help="-L; Smaller values make alignment slower but more sensitive. Default=22"/>
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428 <param name="i" type="text" value="S,1,1.15" label="Set a function governing the interval between seed substrings to use during multiseed alignment (see `Multiseed alignment` section of help below). Also see description of this option below in the help section" help="-i; Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. If the function returns a result less than 1, it is rounded up to 1. Default=`S,1,1.15`"/>
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429 <param name="n_ceil" type="text" value="L,0,0.15" label="Set a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length" help="--n-ceil; For instance, specifying `L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. Reads exceeding this ceiling are filtered out. Default=`L,0,0.15`"/>
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430 <param name="dpad" type="integer" min="0" value="15" label="Pad dynamic programming problems by that many columns on either side to allow gaps" help="--dpad; default=15"/>
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431 <param name="gbar" type="integer" min="0" value="4" label="Disallow gaps within that many positions of the beginning or end of the read" help="--gbar; default=4"/>
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432 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" label="When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value" help="--ignore-quals; input is treated as though all quality values are high; default=False"/>
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433 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" label="Do not attempt to align unpaired reads to the forward (Watson) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
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434 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" label="Do not attempt to align unpaired reads to the reverse (Crick) reference strand" help="In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default=False"/>
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435 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" label="Prevent searching for 1-mismatch end-to-end alignments before using the multiseed heuristic (see `Multiseed alignment` section of help below)" help="--no-1mm-upfront; By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the multiseed heuristic. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the multiseed heuristic, like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the multiseed heuristic, which leads to the expected behavior when combined with options such as `-L` and `-N`. This comes at the expense of speed; Default=False"/>
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436 <conditional name="align_mode">
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437 <param name="align_mode_selector" type="select" display="radio" label="Select between `--local` and `--end-to-end` alignment modes" help="--local and --end-to-end; see help below for detailed explanation; default=--end-to-end">
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438 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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439 <option value="local">Local (--local)</option>
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440 </param>
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441 <when value="end-to-end">
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442 <param name="score_min_ete" type="text" value="L,-0.6,-0.6" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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443 </when>
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444 <when value="local">
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445 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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446 </when>
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447 </conditional>
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448 </when>
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449 <when value="no">
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450 <!-- do nothing -->
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451 </when>
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452 </conditional>
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453 <conditional name="scoring_options">
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454 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See &quot;Scoring Options&quot; section of Help below for information">
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455 <option value="yes">Yes</option>
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456 <option value="no" selected="true">No</option>
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457 </param>
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458 <when value="yes">
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459 <param name="ma" type="integer" value="2" label="Set the match bonus" help="--ma; In `--local` mode match bonus is added to the alignment score for each position where a read character aligns to a reference character and the characters match. Not used in `--end-to-end` mode; Default=2"/>
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460 <param name="mp" type="text" value="6,2" label="Set the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers" help="--mp; A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value; Default=6,2"/>
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461 <param name="np" type="integer" value="1" label="Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`" help="--np; Default=1"/>
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462 <param name="rdg_read_open" type="integer" value="5" label="Set the read gap opening penalty" help="--rdg; this is the first component of --rdg flag - opening penalty; Default=5"/>
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463 <param name="rdg_read_extend" type="integer" value="3" label="Set the read gap extension penalty" help="--rdg; this is the second component of --rdg flag - extension penalty; Default=3"/>
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464 <param name="rfg_ref_open" type="integer" value="5" label="Set the reference gap opening penalty" help="--rfg; this is the first component of --rfg flag - opening penalty; Default=5"/>
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465 <param name="rfg_ref_extend" type="integer" value="3" label="Set the reference gap extension penalty" help="--rfg; this is the second component of --rfg flag - extension penalty; Default=3"/>
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466 </when>
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467 <when value="no">
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468 <!-- do nothing -->
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469 </when>
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470 </conditional>
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471 <conditional name="reporting_options">
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472 <param name="reporting_options_selector" type="select" label="Do you want to use -a or -k options" help="Make sure you understand implications of setting -k and -a. See &quot;Reporting Options&quot; section of Help below for information on -k and -a options">
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473 <option value="no" selected="true">No, do not set</option>
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474 <option value="k">Set -k option and enter -k value</option>
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475 <option value="a">Set -a option</option>
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476 </param>
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477 <when value="no">
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478 <!-- do nothing -->
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479 </when>
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480 <when value="k">
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481 <param name="k" type="integer" min="1" value="1" label="Searches for at most that many distinct, valid alignments for each read" help="-k; see detailed description of this option in the help section below. Note: Bowtie 2 is not designed with large values for `-k` in mind, and when aligning reads to long, repetitive genomes large `-k` can be very, very slow"/>
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482 </when>
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483 <when value="a">
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484 <!-- do nothing here; set -a flag on the command line-->
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485 </when>
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486 </conditional>
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487 <conditional name="effort_options">
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488 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See &quot;Effort Options&quot; section of Help below for information">
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489 <option value="yes">Yes</option>
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490 <option value="no" selected="true">No</option>
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491 </param>
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492 <when value="yes">
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493 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/>
2
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494 <param name="R" type="integer" value="2" min="0" label="Set the maximum number of times Bowtie 2 will `re-seed` reads with repetitive seeds" help="When `re-seeding`, Bowtie 2 simply chooses a new set of reads (same length, same number of mismatches allowed) at different offsets and searches for more alignments. A read is considered to have repetitive seeds if the total number of seed hits divided by the number of seeds that aligned at least once is greater than 300. Default=2"/>
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495 </when>
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496 <when value="no">
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497 <!-- do nothing -->
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498 </when>
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499 </conditional>
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500 <conditional name="sam_options">
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501 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See &quot;Output Options&quot; section of Help below for information">
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502 <option value="yes">Yes</option>
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503 <option value="no" selected="true">No</option>
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504 </param>
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505 <when value="yes">
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506 <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
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507 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
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508 <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
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509 <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
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510 <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
2
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511 </when>
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512 <when value="no">
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513 <!-- do nothing -->
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514 </when>
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515 </conditional>
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516 <conditional name="other_options">
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517 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See &quot;Other Options&quot; section of Help below for information">
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518 <option value="yes">Yes</option>
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519 <option value="no" selected="true">No</option>
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520 </param>
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521 <when value="yes">
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522 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file" help="--reorder; Default=False"/>
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523 <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
5
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524 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
2
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525 </when>
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526 <when value="no">
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527 <!-- do nothing -->
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528 </when>
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529 </conditional>
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530 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/>
0
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531 </when>
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532 </conditional>
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533 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
0
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534 </inputs>
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535 <!-- define outputs -->
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536 <outputs>
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537 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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538 <filter>library['unaligned_file'] is True</filter>
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539 <actions>
5
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540 <conditional name="library.type">
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541 <when value="single">
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542 <action type="format">
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543 <option type="from_param" name="library.input_1" param_attribute="ext" />
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544 </action>
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545 </when>
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546 <when value="paired">
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547 <action type="format">
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548 <option type="from_param" name="library.input_1" param_attribute="ext" />
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549 </action>
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550 </when>
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551 <when value="paired_collection">
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552 <action type="format">
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553 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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554 </action>
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555 </when>
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556 </conditional>
0
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557 </actions>
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558 </data>
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559 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
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560 <filter>library['aligned_file'] is True</filter>
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561 <actions>
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562 <conditional name="library.type">
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563 <when value="single">
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564 <action type="format">
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565 <option type="from_param" name="library.input_1" param_attribute="ext" />
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566 </action>
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567 </when>
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568 <when value="paired">
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569 <action type="format">
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570 <option type="from_param" name="library.input_1" param_attribute="ext" />
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571 </action>
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572 </when>
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573 <when value="paired_collection">
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574 <action type="format">
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575 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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576 </action>
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577 </when>
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578 </conditional>
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579 </actions>
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580 </data>
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581 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
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582 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
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583 <actions>
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584 <conditional name="library.type">
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585 <when value="paired">
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586 <action type="format">
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587 <option type="from_param" name="library.input_2" param_attribute="ext" />
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588 </action>
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589 </when>
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590 <when value="paired_collection">
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591 <action type="format">
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592 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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593 </action>
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594 </when>
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595 </conditional>
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596 </actions>
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597 </data>
0
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598 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
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599 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
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600 <actions>
5
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601 <conditional name="library.type">
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602 <when value="paired">
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603 <action type="format">
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604 <option type="from_param" name="library.input_2" param_attribute="ext" />
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605 </action>
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606 </when>
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607 <when value="paired_collection">
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608 <action type="format">
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609 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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610 </action>
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611 </when>
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612 </conditional>
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613 </actions>
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614 </data>
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615 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
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616 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
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617 <actions>
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618 <conditional name="reference_genome.source">
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619 <when value="indexed">
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620 <action type="metadata" name="dbkey">
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621 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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622 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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623 <filter type="param_value" ref="reference_genome.index" column="0"/>
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624 </option>
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625 </action>
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626 </when>
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627 <when value="history">
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628 <action type="metadata" name="dbkey">
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629 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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630 </action>
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631 </when>
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632 </conditional>
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633 </actions>
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634 </data>
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635 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
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636 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
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637 <actions>
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638 <conditional name="reference_genome.source">
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639 <when value="indexed">
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640 <action type="metadata" name="dbkey">
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641 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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642 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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643 <filter type="param_value" ref="reference_genome.index" column="0"/>
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644 </option>
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645 </action>
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646 </when>
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647 <when value="history">
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648 <action type="metadata" name="dbkey">
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649 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
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650 </action>
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651 </when>
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652 </conditional>
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653 </actions>
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654 </data>
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655 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
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656 <filter>save_mapping_stats is True</filter>
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657 </data>
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658 </outputs>
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659 <tests>
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660 <test>
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661 <!-- test on paired-end datasets -->
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662 <param name="type" value="paired"/>
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663 <param name="paired_options_selector" value="no"/>
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664 <param name="unaligned_file" value="false"/>
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665 <param name="analysis_type_selector" value="simple"/>
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666 <param name="source" value="history" />
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667 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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668 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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669 <param name="own_file" value="bowtie2-ref.fasta" />
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670 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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671 </test>
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672 <test>
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673 <!-- test on paired collection -->
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674 <param name="type" value="paired_collection"/>
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675 <param name="paired_options_selector" value="no"/>
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676 <param name="unaligned_file" value="false"/>
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677 <param name="analysis_type_selector" value="simple"/>
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678 <param name="source" value="history" />
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679 <param name="input_1">
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680 <collection type="paired">
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681 <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
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682 <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
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683 </collection>
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684 </param>
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685 <param name="own_file" value="bowtie2-ref.fasta" />
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686 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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687 </test>
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688 <test>
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689 <!-- test on paired-end datasets with read group info -->
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690 <param name="type" value="paired"/>
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691 <param name="paired_options_selector" value="no"/>
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692 <param name="unaligned_file" value="false"/>
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693 <param name="analysis_type_selector" value="simple"/>
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694 <param name="rg_selector" value="set"/>
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695 <param name="ID" value="rg1"/>
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696 <param name="PL" value="CAPILLARY"/>
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697 <param name="source" value="history" />
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698 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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699 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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700 <param name="own_file" value="bowtie2-ref.fasta" />
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701 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
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702 </test>
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703 <test>
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704 <!-- test on paired-end datasets with stats output -->
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705 <param name="type" value="paired"/>
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706 <param name="paired_options_selector" value="no"/>
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707 <param name="unaligned_file" value="false"/>
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708 <param name="analysis_type_selector" value="simple"/>
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709 <param name="source" value="history" />
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710 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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711 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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712 <param name="own_file" value="bowtie2-ref.fasta" />
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713 <param name="save_mapping_stats" value="true" />
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714 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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715 <output name="mapping_stats">
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716 <assert_contents>
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717 <has_text text="of these" />
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718 </assert_contents>
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iuc
parents: 14
diff changeset
719 </output>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
720 </test>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
721 <test>
17
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parents: 16
diff changeset
722 <!-- test on interleaved dataset -->
15
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
723 <param name="type" value="paired_interleaved"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
724 <!-- <param name="paired_options_selector" value="no"/> -->
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
725 <param name="unaligned_file" value="false"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
726 <param name="analysis_type_selector" value="simple"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
iuc
parents: 14
diff changeset
727 <param name="rg_selector" value="set"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
728 <param name="ID" value="rg1"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
729 <param name="PL" value="CAPILLARY"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
730 <param name="source" value="history" />
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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parents: 14
diff changeset
731 <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
7e0b333f39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit cf554b9b69c32acb484c34fdc60384fa49c7c482
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diff changeset
732 <param name="own_file" value="bowtie2-ref.fasta" />
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parents: 14
diff changeset
733 <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
10
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diff changeset
734 </test>
14
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diff changeset
735 <test>
17
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diff changeset
736 <!-- test on fastqsanger.gz paired-end datasets -->
14
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diff changeset
737 <param name="type" value="paired"/>
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diff changeset
738 <param name="paired_options_selector" value="no"/>
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diff changeset
739 <param name="unaligned_file" value="false"/>
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diff changeset
740 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
741 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
742 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
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diff changeset
743 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
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diff changeset
744 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
745 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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diff changeset
746 </test>
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diff changeset
747 <test>
17
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diff changeset
748 <!-- test on fastqsanger.bz2 paired-end datasets -->
14
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diff changeset
749 <param name="type" value="paired"/>
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diff changeset
750 <param name="paired_options_selector" value="no"/>
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diff changeset
751 <param name="unaligned_file" value="false"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
752 <param name="analysis_type_selector" value="simple"/>
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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parents: 13
diff changeset
753 <param name="source" value="history" />
85f0e9edb32d planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
754 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
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diff changeset
755 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
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diff changeset
756 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
757 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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758 </test>
16
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diff changeset
759 <test>
17
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diff changeset
760 <!-- test on fasta paired-end datasets -->
16
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diff changeset
761 <param name="type" value="paired"/>
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diff changeset
762 <param name="paired_options_selector" value="no"/>
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diff changeset
763 <param name="unaligned_file" value="false"/>
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diff changeset
764 <param name="analysis_type_selector" value="simple"/>
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765 <param name="source" value="history" />
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diff changeset
766 <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
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diff changeset
767 <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
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diff changeset
768 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
769 <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
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770 </test>
0
a03a7ee6cdff Imported from capsule None
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771 </tests>
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772 <help><![CDATA[
0
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773 **Bowtie2 Overview**
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774
2
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775 Bowtie2_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Galaxy wrapper for Bowtie 2 outputs alignments in `BAM format`_, enabling interoperation with a large number of other tools available at this site.
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776 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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777
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778 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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779 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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780 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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781
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782 -----
0
a03a7ee6cdff Imported from capsule None
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783
2
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784 **Selecting reference genomes for Bowtie2**
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785
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786 Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
0
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787
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788 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bowtie2-build utility and are ready to be mapped against.
2
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789 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome from this dropdown will cause Galaxy to first transparently index it using bowtie2-build command, and then run mapping with bowtie2.
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790
2
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791 If your genome of interest is not listed here you have two choices:
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792
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793 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index needs to be added
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794 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
0
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795
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796 ------
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797
2
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798 .. class:: infomark
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diff changeset
799
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800 **Bowtie2 options**
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801
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802 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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803
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804 -----
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805
0
a03a7ee6cdff Imported from capsule None
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806 **Inputs**
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807
15
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diff changeset
808 Bowtie 2 accepts files in Sanger FASTQ format (single or paired-end). Paired-end data can represented as two individual (forward and reverse) datasets, as well as a single interleaved dataset (see an example at the end of the help section).
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809
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810 ------
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811
2
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812 **Input options**::
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813
15
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814 --interleaved
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815 Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair.
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816
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817 -s/--skip <int>
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818 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
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819
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820 -u/--qupto <int>
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821 Align the first `<int>` reads or read pairs from the input (after the
2
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822 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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823
11
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824 -5/--trim5 <int>
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825 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
0
a03a7ee6cdff Imported from capsule None
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826
11
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diff changeset
827 -3/--trim3 <int>
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diff changeset
828 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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diff changeset
829
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diff changeset
830 --phred33
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diff changeset
831 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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diff changeset
832 also called the "Phred+33" encoding, which is used by the very latest Illumina
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833 pipelines.
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diff changeset
834
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diff changeset
835 --phred64
5
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diff changeset
836 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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diff changeset
837 also called the "Phred+64" encoding.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
838
2
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diff changeset
839 --solexa-quals
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diff changeset
840 Convert input qualities from Solexa Phred quality (which can be negative) to
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diff changeset
841 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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diff changeset
842 Pipeline versions (prior to 1.3). Default: off.
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diff changeset
843
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844 --int-quals
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845 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
5
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diff changeset
846 Integers are treated as being on the Phred quality scale unless
2
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847 `--solexa-quals` is also specified. Default: off.
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diff changeset
848
2
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diff changeset
849 ------
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850
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851 **Presets in `--end-to-end` mode**::
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diff changeset
852
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853 --very-fast
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diff changeset
854 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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diff changeset
855
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856 --fast
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857 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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diff changeset
858
2
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diff changeset
859 --sensitive
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860 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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diff changeset
861
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862 --very-sensitive
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diff changeset
863 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
a03a7ee6cdff Imported from capsule None
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864
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865 ------
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866
2
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867 **Presets options in `--local` mode**::
0
a03a7ee6cdff Imported from capsule None
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868
2
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diff changeset
869 --very-fast-local
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diff changeset
870 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
a03a7ee6cdff Imported from capsule None
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871
2
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872 --fast-local
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diff changeset
873 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
a03a7ee6cdff Imported from capsule None
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874
2
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875 --sensitive-local
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876 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
877
2
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diff changeset
878 --very-sensitive-local
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diff changeset
879 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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880
0
a03a7ee6cdff Imported from capsule None
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881 ------
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882
2
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883 **Alignment options**::
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884
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diff changeset
885 -N <int>
5
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diff changeset
886 Sets the number of mismatches to allowed in a seed alignment during multiseed
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diff changeset
887 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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888 (often much slower) but increases sensitivity. Default: 0.
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889
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diff changeset
890 -L <int>
5
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diff changeset
891 Sets the length of the seed substrings to align during multiseed alignment.
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892 Smaller values make alignment slower but more sensitive. Default: the
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diff changeset
893 `--sensitive` preset is used by default, which sets `-L` to 22 in
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
894 `--end-to-end` mode and to 20 in `--local` mode.
2
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diff changeset
895
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diff changeset
896 -i <func>
2
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diff changeset
897 Sets a function governing the interval between seed substrings to use during
5
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diff changeset
898 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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899 length is 10, and the seed interval is 6, the seeds extracted will be:
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diff changeset
900
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diff changeset
901 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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diff changeset
902 Seed 1 fw: TAGCTACGCT
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diff changeset
903 Seed 1 rc: AGCGTAGCTA
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parents: 1
diff changeset
904 Seed 2 fw: CGCTCTACGC
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diff changeset
905 Seed 2 rc: GCGTAGAGCG
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diff changeset
906 Seed 3 fw: ACGCTATCAT
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parents: 1
diff changeset
907 Seed 3 rc: ATGATAGCGT
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diff changeset
908 Seed 4 fw: TCATGCATAA
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diff changeset
909 Seed 4 rc: TTATGCATGA
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diff changeset
910
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diff changeset
911 Since it's best to use longer intervals for longer reads, this parameter sets
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diff changeset
912 the interval as a function of the read length, rather than a single
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diff changeset
913 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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diff changeset
914 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
5
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diff changeset
915 If the function returns a result less than
2
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diff changeset
916 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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diff changeset
917 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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918 in `--local` mode.
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919
11
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diff changeset
920 --n-ceil <func>
2
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diff changeset
921 Sets a function governing the maximum number of ambiguous characters (usually
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
922 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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diff changeset
923 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
924 where x is the read length. Reads exceeding this ceiling are filtered out.
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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parents: 2
diff changeset
925 Default: `L,0,0.15`.
2
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diff changeset
926
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parents: 10
diff changeset
927 --dpad <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
928 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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diff changeset
929 gaps. Default: 15.
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diff changeset
930
11
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diff changeset
931 --gbar <int>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
932 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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933 Default: 4.
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934
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935 --ignore-quals
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936 When calculating a mismatch penalty, always consider the quality value at the
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
937 mismatched position to be the highest possible, regardless of the actual value.
2
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938 I.e. input is treated as though all quality values are high. This is also the
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939 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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940 `-r`, or `-c` modes).
0
a03a7ee6cdff Imported from capsule None
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941
2
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942 --nofw/--norc
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943 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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944 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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945 not attempt to align unpaired reads against the reverse-complement (Crick)
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946 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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947 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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948 paired-end configurations corresponding to fragments from the reverse-complement
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diff changeset
949 (Crick) strand. Default: both strands enabled.
2
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diff changeset
950
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951 --no-1mm-upfront
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diff changeset
952 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
5
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diff changeset
953 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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954 alignments can be found very quickly, and many short read alignments have exact or
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diff changeset
955 near-exact end-to-end alignments. However, this can lead to unexpected
5
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diff changeset
956 alignments when the user also sets options governing the multiseed heuristic,
2
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957 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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958 to the length of the read, the user will be surprised to find 1-mismatch alignments
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959 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
5
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diff changeset
960 alignments before using the multiseed heuristic, which leads to the expected
2
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961 behavior when combined with options such as `-L` and `-N`. This comes at the
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962 expense of speed.
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963
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964 --end-to-end
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965 In this mode, Bowtie 2 requires that the entire read align from one end to the
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966 other, without any trimming (or "soft clipping") of characters from either end.
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967 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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968 are less than or equal to 0, and the greatest possible alignment score is 0.
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969 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
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970
2
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971 --local
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972 In this mode, Bowtie 2 does not require that the entire read align from one end
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973 to the other. Rather, some characters may be omitted ("soft clipped") from the
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974 ends in order to achieve the greatest possible alignment score. The match bonus
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975 `--ma` is used in this mode, and the best possible alignment score is equal to
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976 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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diff changeset
977 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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978 the local version of the preset (`--very-fast-local`). This is mutually
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979 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
11
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980
2
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diff changeset
981 -----
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diff changeset
982
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diff changeset
983 **Scoring options**::
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984
11
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diff changeset
985 --ma <int>
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diff changeset
986 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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987 score for each position where a read character aligns to a reference character
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988 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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989
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diff changeset
990 --mp MX,MN
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diff changeset
991 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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diff changeset
992 number less than or equal to `MX` and greater than or equal to `MN` is
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diff changeset
993 subtracted from the alignment score for each position where a read character
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diff changeset
994 aligns to a reference character, the characters do not match, and neither is an
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diff changeset
995 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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diff changeset
996 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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diff changeset
997 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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998
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diff changeset
999 --np <int>
2
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diff changeset
1000 Sets penalty for positions where the read, reference, or both, contain an
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diff changeset
1001 ambiguous character such as `N`. Default: 1.
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1002
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diff changeset
1003 --rdg <int1>,<int2>
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diff changeset
1004 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1005 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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1006
11
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diff changeset
1007 --rfg <int1>,<int2>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1008 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1009 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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diff changeset
1010 5, 3.
0
a03a7ee6cdff Imported from capsule None
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1011
11
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diff changeset
1012 --score-min <func>
2
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1013 Sets a function governing the minimum alignment score needed for an alignment to
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1014 be considered "valid" (i.e. good enough to report). This is a function of read
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diff changeset
1015 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
5
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
1016 to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and
2
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1017 the default in `--local` mode is `G,20,8`.
11
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diff changeset
1018
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diff changeset
1019 -----
2
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1020
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diff changeset
1021 **Reporting options**::
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1022
11
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diff changeset
1023 -k <int>
2
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1024 By default, `bowtie2` searches for distinct, valid alignments for each read.
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1025 When it finds a valid alignment, it continues looking for alignments that are
2a6cfe8997aa Uploaded from GH
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diff changeset
1026 nearly as good or better. The best alignment found is reported (randomly
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diff changeset
1027 selected from among best if tied). Information about the best alignments is
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1028 used to estimate mapping quality and to set SAM optional fields, such as
2a6cfe8997aa Uploaded from GH
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diff changeset
1029 `AS:i` and `XS:i`.
2a6cfe8997aa Uploaded from GH
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diff changeset
1030
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diff changeset
1031 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
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diff changeset
1032 searches for at most `<int>` distinct, valid alignments for each read. The
2
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diff changeset
1033 search terminates when it can't find more distinct valid alignments, or when it
11
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diff changeset
1034 finds `<int>`, whichever happens first. All alignments found are reported in
2
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1035 descending order by alignment score. The alignment score for a paired-end
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1036 alignment equals the sum of the alignment scores of the individual mates. Each
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1037 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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diff changeset
1038 (which equals 256) set in its FLAGS field. For reads that have more than
11
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1039 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1040 `<int>` alignments reported are the best possible in terms of alignment score.
2
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diff changeset
1041 `-k` is mutually exclusive with `-a`.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1042
2
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1043 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
2a6cfe8997aa Uploaded from GH
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1044 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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1045
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1046 -a
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1047 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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1048 is mutually exclusive with `-k`.
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1049
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1050 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
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diff changeset
1051 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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1052
2
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1053 -----
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1054
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1055 **Effort options**::
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1056
11
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diff changeset
1057 -D <int>
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diff changeset
1058 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1059 moves on, using the alignments found so far. A seed extension "fails" if it
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1060 does not yield a new best or a new second-best alignment. This limit is
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1061 automatically adjusted up when -k or -a are specified. Default: 15.
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1062
11
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diff changeset
1063 -R <int>
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diff changeset
1064 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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1065 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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1066 (same length, same number of mismatches allowed) at different offsets and
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1067 searches for more alignments. A read is considered to have repetitive seeds if
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1068 the total number of seed hits divided by the number of seeds that aligned at
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1069 least once is greater than 300. Default: 2.
11
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1070
2
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diff changeset
1071 -----
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1072
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1073 **Paired-end options**::
0
a03a7ee6cdff Imported from capsule None
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1074
11
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diff changeset
1075 -I/--minins <int>
2
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1076 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
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1077 specified and a paired-end alignment consists of two 20-bp alignments in the
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1078 appropriate orientation with a 20-bp gap between them, that alignment is
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1079 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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1080 be valid in that case. If trimming options `-3` or `-5` are also used, the
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1081 `-I` constraint is applied with respect to the untrimmed mates.
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1082
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1083 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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1084 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1085 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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diff changeset
1086 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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diff changeset
1087 efficient.
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1088
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1089 Default: 0 (essentially imposing no minimum)
2
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1090
11
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diff changeset
1091 -X/--maxins <int>
2
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diff changeset
1092 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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1093 is specified and a paired-end alignment consists of two 20-bp alignments in the
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diff changeset
1094 proper orientation with a 60-bp gap between them, that alignment is considered
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diff changeset
1095 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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diff changeset
1096 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1097 constraint is applied with respect to the untrimmed mates, not the trimmed
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1098 mates.
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diff changeset
1099
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diff changeset
1100 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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diff changeset
1101 run. This is because larger differences bewteen `-I` and `-X` require that
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diff changeset
1102 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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diff changeset
1103 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
2a6cfe8997aa Uploaded from GH
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1104 efficient.
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1105
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1106 Default: 500.
0
a03a7ee6cdff Imported from capsule None
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1107
2
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1108 --fr/--rf/--ff
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diff changeset
1109 The upstream/downstream mate orientations for a valid paired-end alignment
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1110 against the forward reference strand. E.g., if `--fr` is specified and there is
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1111 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1112 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1113 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1114 complement of mate 1 and all other constraints are met, that too is valid.
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1115 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1116 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1117 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1118 for Illumina's Paired-end Sequencing Assay).
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1119
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1120 --no-mixed
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1121 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1122 a pair, it then tries to find alignments for the individual mates. This option
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1123 disables that behavior.
0
a03a7ee6cdff Imported from capsule None
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1124
2
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1125 --no-discordant
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diff changeset
1126 By default, `bowtie2` looks for discordant alignments if it cannot find any
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diff changeset
1127 concordant alignments. A discordant alignment is an alignment where both mates
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1128 align uniquely, but that does not satisfy the paired-end constraints
2a6cfe8997aa Uploaded from GH
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parents: 1
diff changeset
1129 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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diff changeset
1130
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diff changeset
1131 --dovetail
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diff changeset
1132 If the mates "dovetail", that is if one mate alignment extends past the
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parents: 1
diff changeset
1133 beginning of the other such that the wrong mate begins upstream, consider that
5
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diff changeset
1134 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1135
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diff changeset
1136 --no-contain
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diff changeset
1137 If one mate alignment contains the other, consider that to be non-concordant.
5
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diff changeset
1138 Default: a mate can contain the other in a concordant alignment.
2
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1139
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diff changeset
1140 --no-overlap
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diff changeset
1141 If one mate alignment overlaps the other at all, consider that to be
5
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parents: 2
diff changeset
1142 non-concordant. Default: mates can overlap in a concordant alignment.
11
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diff changeset
1143
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1144 ------
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1145
2
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diff changeset
1146 **SAM options**::
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1147
11
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parents: 10
diff changeset
1148 --rg-id <text>
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
1149 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
fa69d5a7b8c8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
1150 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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parents: 1
diff changeset
1151 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
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diff changeset
1152 value set to `<text>`.
0
a03a7ee6cdff Imported from capsule None
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parents:
diff changeset
1153
11
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diff changeset
1154 --rg <text>
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diff changeset
1155 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
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1156 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
5
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diff changeset
1157 must also be specified. This is because the `ID` tag is required by the SAM
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diff changeset
1158 Specification. Specify `--rg` multiple times to set multiple fields. See the
5cfa4b6db588 planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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diff changeset
1159 SAM Specification for details about what fields are legal.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1160
2
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diff changeset
1161 --omit-sec-seq
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1162 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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1163 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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1164 in those fields instead.
11
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diff changeset
1165
2
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1166 -----
0
a03a7ee6cdff Imported from capsule None
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1167
2
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diff changeset
1168 **Other options**::
0
a03a7ee6cdff Imported from capsule None
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1169
2
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1170 --reorder
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1171 Guarantees that output SAM records are printed in an order corresponding to the
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1172 order of the reads in the original input file, even when `-p` is set greater
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1173 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1174 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1175 not specified. Has no effect if `-p` is set to 1, since output order will
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1176 naturally correspond to input order in that case.
0
a03a7ee6cdff Imported from capsule None
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diff changeset
1177
11
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diff changeset
1178 --seed <int>
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diff changeset
1179 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
a03a7ee6cdff Imported from capsule None
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1180
2
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diff changeset
1181 --non-deterministic
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1182 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1183 seeds the generator with a number derived from (a) the read name, (b) the
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1184 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1185 option. This means that if two reads are identical (same name, same
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1186 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1187 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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diff changeset
1188 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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diff changeset
1189 current time. This means that Bowtie 2 will not necessarily report the same
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1190 alignment for two identical reads. This is counter-intuitive for some users,
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1191 but might be more appropriate in situations where the input consists of many
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1192 identical reads.
0
a03a7ee6cdff Imported from capsule None
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1193
15
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1194 -----
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1195
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1196
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diff changeset
1197 **Paired-end (and mate-pair) data in fastq format**
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1198
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diff changeset
1199 Paired end datasets can be represented as two individual datasets:
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1200
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diff changeset
1201 First dataset::
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diff changeset
1202
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1203 @1/1
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1204 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1205 +
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1206 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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diff changeset
1207 @2/1
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1208 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1209 +
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1210 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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1211
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diff changeset
1212 Second dataset::
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1213
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1214 @1/2
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diff changeset
1215 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1216 +
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1217 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
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diff changeset
1218 @2/2
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1219 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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1220 +
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1221 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
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1222
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1223 Or a single *interleaved* dataset::
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1224
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1225 @1/1
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1226 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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1227 +
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1228 EGGEGGGDFGEEEAEECGDEGGFEEGEFGBEEDDECFEFDD@CDD<ED
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diff changeset
1229 @1/2
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diff changeset
1230 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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diff changeset
1231 +
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diff changeset
1232 GHHHDFDFGFGEGFBGEGGEGEGGGHGFGHFHFHHHHHHHEF?EFEFF
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diff changeset
1233 @2/1
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1234 AGGGATGTGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTA
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diff changeset
1235 +
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diff changeset
1236 HHHHHHEGFHEEFEEHEEHHGGEGGGGEFGFGGGGHHHHFBEEEEEFG
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diff changeset
1237 @2/2
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diff changeset
1238 CCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAAC
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diff changeset
1239 +
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1240 HHHHHHHHHHHHHGHHHHHHGHHHHHHHHHHHFHHHFHHHHHHHHHHH
11
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diff changeset
1241 ]]></help>
2
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1242 <citations>
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69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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1243 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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1244 <citation type="doi">10.1038/nmeth.1923</citation>
69f044db2445 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 0f9578a65e86cc159aadf1a9b37aaf3621f19456
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1245 </citations>
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a03a7ee6cdff Imported from capsule None
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1246 </tool>