annotate bowtie2_wrapper.xml @ 14:937aa69e715f draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
author devteam
date Wed, 12 Apr 2017 17:09:42 -0400
parents 12450efac659
children 43d12513224b
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14
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1 <tool id="bowtie2" name="Bowtie2" version="2.3.0.1" 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>read_group_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="2.3.0">bowtie2</requirement>
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8 <requirement type="package" version="1.3.1">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 ## prepare bowtie2 index
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13 #set index_path = ''
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14 #if str($reference_genome.source) == "history":
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15 bowtie2-build --threads \${GALAXY_SLOTS:-4} '$reference_genome.own_file' genome &&
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16 ln -s -f '$reference_genome.own_file' genome.fa &&
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17 #set index_path = 'genome'
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18 #else:
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19 #set index_path = $reference_genome.index.fields.path
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20 #end if
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21
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22 ## Link in the input files, so bowtie2 can tell their type
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23
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24 #set compressed="False"
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25 #if str($library.type) == 'paired':
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26 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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27 #set read1 = "input_f.fastq.gz"
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28 #set compressed = "GZ"
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29 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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30 #set read1 = "input_f.fastq.bz2"
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31 #set compressed = "BZ2"
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32 #else:
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33 #set read1 = "input_f.fastq"
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34 #end if
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35 ln -f -s '${library.input_1}' ${read1} &&
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36
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37 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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38 #set read2 = "input_r.fastq.gz"
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39 #set compressed = "GZ"
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40 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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41 #set read2 = "input_r.fastq.bz2"
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42 #set compressed = "BZ2"
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43 #else:
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44 #set read2 = "input_r.fastq"
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45 #end if
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46 ln -f -s '${library.input_2}' ${read2} &&
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47 #else if str($library.type) == 'paired_collection':
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48 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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49 #set read1 = "input_f.fastq.gz"
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50 #set compressed = "GZ"
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51 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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52 #set read1 = "input_f.fastq.bz2"
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53 #set compressed = "BZ2"
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54 #else:
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55 #set read1 = "input_f.fastq"
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56 #end if
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57 ln -s '${library.input_1.forward}' ${read1} &&
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58
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59 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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60 #set read2 = "input_r.fastq.gz"
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61 #set compressed = "GZ"
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62 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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63 #set read2 = "input_r.fastq.bz2"
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64 #set compressed = "BZ2"
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65 #else:
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66 #set read2 = "input_r.fastq"
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67 #end if
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68 ln -s '${library.input_1.reverse}' ${read2} &&
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69 #else:
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70 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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71 #set read1 = "input_f.fastq.gz"
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72 #set compressed = "GZ"
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73 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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74 #set read1 = "input_f.fastq.bz2"
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75 #set compressed = "BZ2"
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76 #else:
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77 #set read1 = "input_f.fastq"
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78 #end if
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79 ln -s '${library.input_1}' ${read1} &&
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80 #end if
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81
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82 ## execute bowtie2
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83
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84 bowtie2
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85
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86 ## number of threads
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87 -p \${GALAXY_SLOTS:-4}
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88
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89 ## index file path
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90 -x '$index_path'
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91
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92 ## Fastq inputs
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93 #if str( $library.type ) == "single":
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94 -U '${read1}'
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95 #if str( $library.unaligned_file ) == "true":
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96 #if $compressed == "GZ":
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97 --un-gz '${output_unaligned_reads_l}'
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98 #else if $compressed == "BZ2":
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99 --un-bz2 '${output_unaligned_reads_l}'
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100 #else:
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101 --un '${output_unaligned_reads_l}'
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102 #end if
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103 #end if
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104 #if str( $library.aligned_file ) == "true":
14
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105 #if $compressed == "GZ":
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106 --al-gz '${output_aligned_reads_l}'
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107 #else if $compressed == "BZ2":
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108 --al-bz2 '${output_aligned_reads_l}'
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109 #else:
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110 --al '${output_aligned_reads_l}'
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111 #end if
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112 #end if
14
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113 #else:
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114 -1 '${read1}'
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115 -2 '${read2}'
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116 #if str( $library.unaligned_file ) == "true":
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117 #if $compressed == "GZ":
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118 --un-conc-gz '${output_unaligned_reads_l}'
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119 #else if $compressed == "BZ2":
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120 --un-conc-bz2 '${output_unaligned_reads_l}'
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121 #else:
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122 --un-conc '${output_unaligned_reads_l}'
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123 #end if
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124 #end if
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125 #if str( $library.aligned_file ) == "true":
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126 #if $compressed == "GZ":
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127 --al-conc-gz '${output_aligned_reads_l}'
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128 #else if $compressed == "BZ2":
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129 --al-conc-bz2 '${output_aligned_reads_l}'
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130 #else:
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131 --al-conc '${output_aligned_reads_l}'
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132 #end if
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133 #end if
2
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134 #if str( $library.paired_options.paired_options_selector ) == "yes":
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135 -I "${library.paired_options.I}"
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136 -X "${library.paired_options.X}"
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137 ${library.paired_options.fr_rf_ff}
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138 ${library.paired_options.no_mixed}
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139 ${library.paired_options.no_discordant}
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140 ${library.paired_options.dovetail}
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141 ${library.paired_options.no_contain}
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142 ${library.paired_options.no_overlap}
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143 #end if
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144 #end if
7
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145
5
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146 ## Read group information.
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147 @define_read_group_helpers@
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148 #if str( $library.type ) == "single":
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149 #set $rg_auto_name = $read_group_name_default($library.input_1)
5
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150 #elif str( $library.type ) == "paired":
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151 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
5
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152 #else
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153 #set $rg_auto_name = $read_group_name_default($library.input_1)
5
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154 #end if
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155 @set_use_rg_var@
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156 @set_read_group_vars@
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157 #if $use_rg
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158 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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159 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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160 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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161 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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162 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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163 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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164 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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165 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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166 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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167 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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168 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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169 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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170 #end if
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171
2
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172 ## Analysis type
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173 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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174 $analysis_type.presets
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175 #elif str( $analysis_type.analysis_type_selector ) == "full":
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176 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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177 --skip "${analysis_type.input_options.skip}"
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178 --qupto "${analysis_type.input_options.qupto}"
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179 --trim5 "${analysis_type.input_options.trim5}"
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180 --trim3 "${analysis_type.input_options.trim3}"
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181 ${analysis_type.input_options.qv_encoding}
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182 ${analysis_type.input_options.solexa_quals}
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183 ${analysis_type.input_options.int_quals}
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184 #end if
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185
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186 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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187 -N "${analysis_type.alignment_options.N}"
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188 -L "${analysis_type.alignment_options.L}"
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189 -i "${analysis_type.alignment_options.i}"
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190 --n-ceil "${analysis_type.alignment_options.n_ceil}"
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191 --dpad "${analysis_type.alignment_options.dpad}"
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192 --gbar "${analysis_type.alignment_options.gbar}"
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193 ${analysis_type.alignment_options.ignore_quals}
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194 ${analysis_type.alignment_options.nofw}
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195 ${analysis_type.alignment_options.norc}
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196 ${analysis_type.alignment_options.no_1mm_upfront}
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197 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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198 --end-to-end
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199 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}"
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200 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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201 --local
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202 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
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203 #end if
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204 #end if
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205
2
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206 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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207 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
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208 --ma "${analysis_type.scoring_options.ma}"
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209 #end if
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210 --mp "${analysis_type.scoring_options.mp}"
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211 --np "${analysis_type.scoring_options.np}"
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212 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
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213 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
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214 #end if
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215
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216 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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217 -k "${analysis_type.reporting_options.k}"
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218 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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219 -a
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220 #end if
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221
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222 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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223 -D "${analysis_type.effort_options.D}"
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224 -R "${analysis_type.effort_options.R}"
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225 #end if
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226
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227 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
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228 ${analysis_type.sam_options.no_unal}
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229 ${analysis_type.sam_options.omit_sec_seq}
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230 #end if
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231
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232 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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233 ${analysis_type.other_options.reorder}
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234 ${analysis_type.other_options.non_deterministic}
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235 --seed "${analysis_type.other_options.seed}"
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236 #end if
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237
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238 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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239 ${analysis_type.cline}
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240 #end if
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241
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242 ## mapping stats (i.e. stderr from bowtie2)
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243 #if $save_mapping_stats
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244 2> '$mapping_stats'
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245 #end if
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246
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247 ## output file
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248 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
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249 | samtools sort -O bam -o '$output'
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250 #else
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251 > '$output_sam'
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252 #end if
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253
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254 ## rename unaligned sequence files
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255 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
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256 #from os.path import splitext
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257 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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258 && mv "${ _unaligned_root }.1${_unaligned_ext}" '$output_unaligned_reads_l'
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259 && mv "${ _unaligned_root }.2${_unaligned_ext}" '$output_unaligned_reads_r'
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260 #end if
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261 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
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262 #from os.path import splitext
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263 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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264 && mv "${ _aligned_root }.1${_aligned_ext}" '$output_aligned_reads_l'
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265 && mv "${ _aligned_root }.2${_aligned_ext}" '$output_aligned_reads_r'
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266 #end if
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267
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268 ]]></command>
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269 <inputs>
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270 <!-- single/paired -->
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271 <conditional name="library">
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272 <param name="type" type="select" label="Is this single or paired library">
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273 <option value="single">Single-end</option>
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274 <option value="paired">Paired-end</option>
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275 <option value="paired_collection">Paired-end Dataset Collection</option>
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276 </param>
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277
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278 <when value="single">
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279 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
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280 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" />
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281 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" />
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282 </when>
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283 <when value="paired">
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284 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
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285 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
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286 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" />
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287 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" />
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288 <conditional name="paired_options">
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289 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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290 <option value="no" selected="True">No</option>
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291 <option value="yes">Yes</option>
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292 </param>
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293 <when value="yes">
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294 <param name="I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" help="-I/--minins; E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/>
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295 <param name="X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" help="-X/--maxins; E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/>
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296 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
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297 <option value="--fr" selected="True">--fr</option>
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298 <option value="--rf">--rf</option>
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299 <option value="--ff">--ff</option>
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300 </param>
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301 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
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302 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
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303 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
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304 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
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305 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
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306 </when>
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307 <when value="no">
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308 <!-- do nothing -->
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309 </when>
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310 </conditional>
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311 </when>
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312 <when value="paired_collection">
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313 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" />
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314 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" help="--un/--un-conc (possibly with -gz or -bz2); This triggers --un parameter for single reads and --un-conc for paired reads" />
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315 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" help="--al/--al-conc (possibly with -gz or -bz2); This triggers --al parameter for single reads and --al-conc for paired reads" />
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316 <conditional name="paired_options">
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317 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See &quot;Alignment Options&quot; section of Help below for information">
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318 <option value="no" selected="True">No</option>
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319 <option value="yes">Yes</option>
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320 </param>
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321 <when value="yes">
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322 <param name="I" type="integer" value="0" min="0" label="Set the minimum fragment length for valid paired-end alignments" help="-I/--minins; E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as `-X` is also satisfied). A 19-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-I` constraint is applied with respect to the untrimmed mates. The larger the difference between `-I` and `-X`, the slower Bowtie 2 will run. This is because larger differences bewteen `-I` and `-X` require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default=0"/>
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323 <param name="X" type="integer" value="500" min="0" label="Set the maximum fragment length for valid paired-end alignments" help="-X/--maxins; E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in that case. If trimming options `-3` or `-5` are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates; Default=500"/>
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324 <param name="fr_rf_ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand" help="--fr, --rf, or --ff; E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
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325 <option value="--fr" selected="True">--fr</option>
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326 <option value="--rf">--rf</option>
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327 <option value="--ff">--ff</option>
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328 </param>
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329 <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="--no-mixed; By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default=False"/>
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330 <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default=False"/>
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331 <param name="dovetail" type="boolean" truevalue="--dovetail" falsevalue="" checked="False" label="Allow mate dovetailing" help="--dovetail; If the mates `dovetail`, that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. Default=False"/>
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332 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Disallow one mate alignment to contain another" help="--no-contain; If one mate alignment contains the other, consider that to be non-concordant. Default=False"/>
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333 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Disallow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/>
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334 </when>
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335 <when value="no">
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336 <!-- do nothing -->
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337 </when>
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338 </conditional>
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339 </when>
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340 </conditional>
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341
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342 <!-- reference genome -->
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343 <conditional name="reference_genome">
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344 <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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345 <option value="indexed">Use a built-in genome index</option>
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346 <option value="history">Use a genome from the history and build index</option>
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347 </param>
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348 <when value="indexed">
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349 <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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350 <options from_data_table="bowtie2_indexes">
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351 <filter type="sort_by" column="2"/>
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352 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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353 </options>
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354 </param>
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355 </when>
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356 <when value="history">
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357 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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358 </when>
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359 </conditional>
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360
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361 <!-- read group settings -->
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362 <expand macro="read_group_conditional" />
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363 <conditional name="analysis_type">
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364 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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365 <option value="simple">1: Default setting only</option>
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366 <option value="full">2: Full parameter list</option>
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367 </param>
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368 <when value="simple">
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369 <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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370 <option value="no_presets" selected="True">No, just use defaults</option>
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371 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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372 <option value="--fast">Fast end-to-end (--fast)</option>
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373 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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374 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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375 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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376 <option value="--fast-local">Fast local (--fast-local)</option>
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377 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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378 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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379 </param>
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380 </when>
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381 <when value="full">
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382 <conditional name="input_options">
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383 <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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384 <option value="yes">Yes</option>
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385 <option value="no" selected="true">No</option>
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386 </param>
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387 <when value="yes">
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388 <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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389 <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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390 <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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391 <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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392 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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393 <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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394 <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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395 </param>
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396 <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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397 <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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398 </when>
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399 <when value="no">
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400 <!-- do nothing -->
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401 </when>
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402 </conditional>
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403 <conditional name="alignment_options">
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404 <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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405 <option value="yes">Yes</option>
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406 <option value="no" selected="true">No</option>
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407 </param>
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408 <when value="yes">
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409 <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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410 <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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411 <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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412 <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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413 <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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414 <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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415 <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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416 <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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417 <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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418 <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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419 <conditional name="align_mode">
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420 <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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421 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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422 <option value="local">Local (--local)</option>
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423 </param>
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424 <when value="end-to-end">
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425 <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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426 </when>
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427 <when value="local">
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428 <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`"/>
2
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429 </when>
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430 </conditional>
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431 </when>
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432 <when value="no">
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parents: 0
diff changeset
433 <!-- do nothing -->
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434 </when>
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435 </conditional>
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436 <conditional name="scoring_options">
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437 <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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438 <option value="yes">Yes</option>
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439 <option value="no" selected="true">No</option>
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440 </param>
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441 <when value="yes">
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442 <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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443 <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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444 <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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445 <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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446 <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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447 <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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448 <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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449 </when>
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450 <when value="no">
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diff changeset
451 <!-- do nothing -->
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452 </when>
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453 </conditional>
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454 <conditional name="reporting_options">
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455 <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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456 <option value="no" selected="true">No, do not set</option>
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457 <option value="k">Set -k option and enter -k value</option>
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458 <option value="a">Set -a option</option>
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459 </param>
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460 <when value="no">
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461 <!-- do nothing -->
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462 </when>
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463 <when value="k">
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464 <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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465 </when>
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466 <when value="a">
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467 <!-- do nothing here; set -a flag on the command line-->
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468 </when>
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469 </conditional>
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470 <conditional name="effort_options">
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471 <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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472 <option value="yes">Yes</option>
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473 <option value="no" selected="true">No</option>
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474 </param>
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475 <when value="yes">
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476 <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"/>
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477 <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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478 </when>
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479 <when value="no">
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parents: 0
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480 <!-- do nothing -->
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481 </when>
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482 </conditional>
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483
2
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parents: 0
diff changeset
484 <conditional name="sam_options">
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485 <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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parents: 0
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486 <option value="yes">Yes</option>
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487 <option value="no" selected="true">No</option>
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488 </param>
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parents: 0
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489 <when value="yes">
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490 <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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491 <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"/>
2
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parents: 0
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492 </when>
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parents: 0
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493 <when value="no">
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parents: 0
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494 <!-- do nothing -->
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parents: 0
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495 </when>
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496 </conditional>
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parents: 0
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497 <conditional name="other_options">
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498 <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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parents: 0
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499 <option value="yes">Yes</option>
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500 <option value="no" selected="true">No</option>
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501 </param>
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502 <when value="yes">
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503 <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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parents: 0
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504 <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"/>
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parents: 2
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505 <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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parents: 0
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506 </when>
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parents: 0
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507 <when value="no">
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parents: 0
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508 <!-- do nothing -->
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509 </when>
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510 </conditional>
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511 <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."/>
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512 </when>
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513 </conditional>
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514 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
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515 </inputs>
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516
96d2e31a3938 Imported from capsule None
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517 <!-- define outputs -->
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518
0
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519 <outputs>
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520
0
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521 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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522 <filter>library['unaligned_file'] is True</filter>
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523 <actions>
7
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524 <conditional name="library.type">
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525 <when value="single">
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526 <action type="format">
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527 <option type="from_param" name="library.input_1" param_attribute="ext" />
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528 </action>
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529 </when>
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530 <when value="paired">
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531 <action type="format">
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532 <option type="from_param" name="library.input_1" param_attribute="ext" />
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533 </action>
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534 </when>
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535 <when value="paired_collection">
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536 <action type="format">
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537 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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538 </action>
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539 </when>
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540 </conditional>
0
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541 </actions>
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542 </data>
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543 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
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544 <filter>library['aligned_file'] is True</filter>
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545 <actions>
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546 <conditional name="library.type">
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547 <when value="single">
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548 <action type="format">
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549 <option type="from_param" name="library.input_1" param_attribute="ext" />
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550 </action>
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551 </when>
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552 <when value="paired">
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553 <action type="format">
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554 <option type="from_param" name="library.input_1" param_attribute="ext" />
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555 </action>
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556 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
557 <when value="paired_collection">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
558 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
559 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
560 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
561 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
562 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
563 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
564 </data>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
565 <data format="fastqsanger" name="output_aligned_reads_r" label="${tool.name} on ${on_string}: aligned reads (R)">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
566 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['aligned_file'] is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
567 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
568 <conditional name="library.type">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
569 <when value="paired">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
570 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
571 <option type="from_param" name="library.input_2" param_attribute="ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
572 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
573 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
574 <when value="paired_collection">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
575 <action type="format">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
576 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
577 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
578 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
579 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
580 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
581 </data>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
582 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)">
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
583 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
584 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
585 <conditional name="library.type">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
586 <when value="paired">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
587 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
588 <option type="from_param" name="library.input_2" param_attribute="ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
589 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
590 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
591 <when value="paired_collection">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
592 <action type="format">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
593 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
594 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
595 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
596 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
597 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
598 </data>
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
599
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
600 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)">
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
601 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
602 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
603 <conditional name="reference_genome.source">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
604 <when value="indexed">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
605 <action type="metadata" name="dbkey">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
606 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
607 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
608 <filter type="param_value" ref="reference_genome.index" column="0"/>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
609 </option>
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parents: 6
diff changeset
610 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
611 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
612 <when value="history">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
613 <action type="metadata" name="dbkey">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
614 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
615 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
616 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
617 </conditional>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
618 </actions>
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parents: 6
diff changeset
619 </data>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
620
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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parents: 6
diff changeset
621 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)">
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
622 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
623 <actions>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
624 <conditional name="reference_genome.source">
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
625 <when value="indexed">
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
626 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
627 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
628 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
629 <filter type="param_value" ref="reference_genome.index" column="0"/>
96d2e31a3938 Imported from capsule None
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parents:
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630 </option>
96d2e31a3938 Imported from capsule None
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parents:
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631 </action>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
632 </when>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
633 <when value="history">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
634 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
635 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
636 </action>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
637 </when>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
638 </conditional>
96d2e31a3938 Imported from capsule None
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parents:
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639 </actions>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
640 </data>
10
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parents: 8
diff changeset
641 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
642 <filter>save_mapping_stats is True</filter>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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diff changeset
643 </data>
3
ceb6467e276c Uploaded
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parents: 2
diff changeset
644
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
645 </outputs>
96d2e31a3938 Imported from capsule None
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parents:
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646
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
647 <tests>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
648 <test>
96d2e31a3938 Imported from capsule None
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649 <!-- basic test on single paired default run -->
2
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parents: 0
diff changeset
650 <param name="type" value="paired"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
651 <param name="selection" value="no"/>
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
652 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
653 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
654 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
655 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
656 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
657 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
658 <param name="own_file" value="bowtie2-ref.fasta" />
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
659 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
660 </test>
5
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parents: 4
diff changeset
661 <test>
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parents: 4
diff changeset
662 <!-- basic test on single paired default run -->
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents: 4
diff changeset
663 <param name="type" value="paired"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents: 4
diff changeset
664 <param name="selection" value="no"/>
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parents: 4
diff changeset
665 <param name="paired_options_selector" value="no"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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parents: 4
diff changeset
666 <param name="unaligned_file" value="false"/>
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667 <param name="analysis_type_selector" value="simple"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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668 <param name="rg_selector" value="set"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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669 <param name="ID" value="rg1"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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diff changeset
670 <param name="PL" value="CAPILLARY"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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671 <param name="source" value="history" />
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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672 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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673 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
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674 <param name="own_file" value="bowtie2-ref.fasta" />
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675 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
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676 </test>
10
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677 <test>
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678 <!-- basic test on single paired default run with stats-->
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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679 <param name="type" value="paired"/>
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680 <param name="selection" value="no"/>
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681 <param name="paired_options_selector" value="no"/>
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diff changeset
682 <param name="unaligned_file" value="false"/>
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683 <param name="analysis_type_selector" value="simple"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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diff changeset
684 <param name="source" value="history" />
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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diff changeset
685 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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diff changeset
686 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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687 <param name="own_file" value="bowtie2-ref.fasta" />
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diff changeset
688 <param name="save_mapping_stats" value="true" />
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diff changeset
689 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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diff changeset
690 <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
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691 </test>
14
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diff changeset
692 <test>
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693 <!-- test fastqsanger.gz input -->
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694 <param name="type" value="paired"/>
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695 <param name="selection" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
696 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
697 <param name="unaligned_file" value="false"/>
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diff changeset
698 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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699 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
700 <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
701 <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
702 <param name="own_file" value="bowtie2-ref.fasta" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
703 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
704 </test>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
705 <test>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
706 <!-- test fastqsanger.bz2 input -->
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
707 <param name="type" value="paired"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
708 <param name="selection" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
709 <param name="paired_options_selector" value="no"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
710 <param name="unaligned_file" value="false"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
711 <param name="analysis_type_selector" value="simple"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
712 <param name="source" value="history" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
713 <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
714 <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
715 <param name="own_file" value="bowtie2-ref.fasta" />
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
716 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
937aa69e715f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 954b2052cb74a0bc88f65df37f429ff27c45ea8f
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diff changeset
717 </test>
0
96d2e31a3938 Imported from capsule None
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718 </tests>
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719
11
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diff changeset
720 <help><![CDATA[
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721
0
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722 **Bowtie2 Overview**
11
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723
2
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724 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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725 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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726
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727 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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728 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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729 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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730
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731 -----
0
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732
2
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733 **Selecting reference genomes for Bowtie2**
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734
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735 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
96d2e31a3938 Imported from capsule None
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736
11
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diff changeset
737 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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738 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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739
2
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740 If your genome of interest is not listed here you have two choices:
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741
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742 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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743 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.
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744
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745 ------
96d2e31a3938 Imported from capsule None
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746
2
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747 .. class:: infomark
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748
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749 **Bowtie2 options**
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750
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751 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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752
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753 -----
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754
0
96d2e31a3938 Imported from capsule None
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755 **Inputs**
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756
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757 Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files.
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758
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759 ------
96d2e31a3938 Imported from capsule None
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760
2
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761 **Input options**::
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762
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763 -s/--skip <int>
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764 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
2
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765
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766 -u/--qupto <int>
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767 Align the first `<int>` reads or read pairs from the input (after the
2
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768 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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769
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770 -5/--trim5 <int>
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771 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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772
11
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diff changeset
773 -3/--trim3 <int>
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diff changeset
774 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
2
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775
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776 --phred33
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diff changeset
777 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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778 also called the "Phred+33" encoding, which is used by the very latest Illumina
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779 pipelines.
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780
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781 --phred64
3
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782 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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783 also called the "Phred+64" encoding.
0
96d2e31a3938 Imported from capsule None
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784
2
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785 --solexa-quals
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786 Convert input qualities from Solexa Phred quality (which can be negative) to
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diff changeset
787 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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788 Pipeline versions (prior to 1.3). Default: off.
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789
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790 --int-quals
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791 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`....
3
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792 Integers are treated as being on the Phred quality scale unless
2
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793 `--solexa-quals` is also specified. Default: off.
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794
2
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795 ------
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796
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797 **Presets in `--end-to-end` mode**::
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798
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799 --very-fast
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diff changeset
800 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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801
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802 --fast
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803 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
11
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804
2
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805 --sensitive
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806 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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807
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808 --very-sensitive
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809 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
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810
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811 ------
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812
2
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813 **Presets options in `--local` mode**::
0
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814
2
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815 --very-fast-local
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816 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
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817
2
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818 --fast-local
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819 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
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820
2
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821 --sensitive-local
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822 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
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823
2
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824 --very-sensitive-local
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825 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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826
0
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827 ------
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828
2
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829 **Alignment options**::
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830
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831 -N <int>
3
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832 Sets the number of mismatches to allowed in a seed alignment during multiseed
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833 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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834 (often much slower) but increases sensitivity. Default: 0.
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835
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836 -L <int>
3
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837 Sets the length of the seed substrings to align during multiseed alignment.
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838 Smaller values make alignment slower but more sensitive. Default: the
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839 `--sensitive` preset is used by default, which sets `-L` to 22 in
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840 `--end-to-end` mode and to 20 in `--local` mode.
2
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841
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842 -i <func>
2
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843 Sets a function governing the interval between seed substrings to use during
3
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844 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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845 length is 10, and the seed interval is 6, the seeds extracted will be:
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846
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847 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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848 Seed 1 fw: TAGCTACGCT
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849 Seed 1 rc: AGCGTAGCTA
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850 Seed 2 fw: CGCTCTACGC
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851 Seed 2 rc: GCGTAGAGCG
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852 Seed 3 fw: ACGCTATCAT
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853 Seed 3 rc: ATGATAGCGT
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854 Seed 4 fw: TCATGCATAA
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855 Seed 4 rc: TTATGCATGA
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856
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857 Since it's best to use longer intervals for longer reads, this parameter sets
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858 the interval as a function of the read length, rather than a single
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859 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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860 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
3
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861 If the function returns a result less than
2
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862 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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863 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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864 in `--local` mode.
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865
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866 --n-ceil <func>
2
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867 Sets a function governing the maximum number of ambiguous characters (usually
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868 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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869 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
3
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870 where x is the read length. Reads exceeding this ceiling are filtered out.
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871 Default: `L,0,0.15`.
2
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872
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873 --dpad <int>
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874 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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875 gaps. Default: 15.
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876
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diff changeset
877 --gbar <int>
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878 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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879 Default: 4.
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880
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881 --ignore-quals
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882 When calculating a mismatch penalty, always consider the quality value at the
11
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883 mismatched position to be the highest possible, regardless of the actual value.
2
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884 I.e. input is treated as though all quality values are high. This is also the
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885 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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886 `-r`, or `-c` modes).
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887
2
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888 --nofw/--norc
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889 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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diff changeset
890 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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891 not attempt to align unpaired reads against the reverse-complement (Crick)
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892 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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893 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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894 paired-end configurations corresponding to fragments from the reverse-complement
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895 (Crick) strand. Default: both strands enabled.
2
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896
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897 --no-1mm-upfront
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898 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
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899 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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900 alignments can be found very quickly, and many short read alignments have exact or
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901 near-exact end-to-end alignments. However, this can lead to unexpected
3
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902 alignments when the user also sets options governing the multiseed heuristic,
2
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903 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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904 to the length of the read, the user will be surprised to find 1-mismatch alignments
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905 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
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906 alignments before using the multiseed heuristic, which leads to the expected
2
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907 behavior when combined with options such as `-L` and `-N`. This comes at the
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908 expense of speed.
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909
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910 --end-to-end
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911 In this mode, Bowtie 2 requires that the entire read align from one end to the
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912 other, without any trimming (or "soft clipping") of characters from either end.
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913 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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914 are less than or equal to 0, and the greatest possible alignment score is 0.
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915 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
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916
2
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917 --local
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918 In this mode, Bowtie 2 does not require that the entire read align from one end
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919 to the other. Rather, some characters may be omitted ("soft clipped") from the
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920 ends in order to achieve the greatest possible alignment score. The match bonus
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921 `--ma` is used in this mode, and the best possible alignment score is equal to
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922 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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923 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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924 the local version of the preset (`--very-fast-local`). This is mutually
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925 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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926
2
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927 -----
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928
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929 **Scoring options**::
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930
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931 --ma <int>
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932 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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933 score for each position where a read character aligns to a reference character
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934 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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935
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936 --mp MX,MN
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937 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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938 number less than or equal to `MX` and greater than or equal to `MN` is
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939 subtracted from the alignment score for each position where a read character
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940 aligns to a reference character, the characters do not match, and neither is an
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941 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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diff changeset
942 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
c1ec08cb34f9 Uploaded
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diff changeset
943 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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parents: 0
diff changeset
944
11
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diff changeset
945 --np <int>
2
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parents: 0
diff changeset
946 Sets penalty for positions where the read, reference, or both, contain an
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
947 ambiguous character such as `N`. Default: 1.
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parents: 0
diff changeset
948
11
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devteam
parents: 10
diff changeset
949 --rdg <int1>,<int2>
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parents: 10
diff changeset
950 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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parents: 10
diff changeset
951 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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parents: 0
diff changeset
952
11
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parents: 10
diff changeset
953 --rfg <int1>,<int2>
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parents: 10
diff changeset
954 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
955 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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diff changeset
956 5, 3.
0
96d2e31a3938 Imported from capsule None
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diff changeset
957
11
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parents: 10
diff changeset
958 --score-min <func>
2
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parents: 0
diff changeset
959 Sets a function governing the minimum alignment score needed for an alignment to
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960 be considered "valid" (i.e. good enough to report). This is a function of read
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961 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
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diff changeset
962 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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diff changeset
963 the default in `--local` mode is `G,20,8`.
11
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diff changeset
964
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diff changeset
965 -----
2
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966
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diff changeset
967 **Reporting options**::
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968
11
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diff changeset
969 -k <int>
2
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970 By default, `bowtie2` searches for distinct, valid alignments for each read.
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971 When it finds a valid alignment, it continues looking for alignments that are
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972 nearly as good or better. The best alignment found is reported (randomly
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973 selected from among best if tied). Information about the best alignments is
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974 used to estimate mapping quality and to set SAM optional fields, such as
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975 `AS:i` and `XS:i`.
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976
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977 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
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diff changeset
978 searches for at most `<int>` distinct, valid alignments for each read. The
2
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979 search terminates when it can't find more distinct valid alignments, or when it
11
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diff changeset
980 finds `<int>`, whichever happens first. All alignments found are reported in
2
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diff changeset
981 descending order by alignment score. The alignment score for a paired-end
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982 alignment equals the sum of the alignment scores of the individual mates. Each
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983 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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984 (which equals 256) set in its FLAGS field. For reads that have more than
11
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diff changeset
985 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
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diff changeset
986 `<int>` alignments reported are the best possible in terms of alignment score.
2
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987 `-k` is mutually exclusive with `-a`.
0
96d2e31a3938 Imported from capsule None
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988
2
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989 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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990 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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991
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992 -a
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993 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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994 is mutually exclusive with `-k`.
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995
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996 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
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diff changeset
997 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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998
2
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999 -----
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1000
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1001 **Effort options**::
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1002
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diff changeset
1003 -D <int>
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diff changeset
1004 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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1005 moves on, using the alignments found so far. A seed extension "fails" if it
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1006 does not yield a new best or a new second-best alignment. This limit is
c1ec08cb34f9 Uploaded
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1007 automatically adjusted up when -k or -a are specified. Default: 15.
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1008
11
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diff changeset
1009 -R <int>
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diff changeset
1010 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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1011 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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1012 (same length, same number of mismatches allowed) at different offsets and
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1013 searches for more alignments. A read is considered to have repetitive seeds if
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1014 the total number of seed hits divided by the number of seeds that aligned at
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1015 least once is greater than 300. Default: 2.
11
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1016
2
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diff changeset
1017 -----
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1018
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1019 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
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parents:
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1020
11
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diff changeset
1021 -I/--minins <int>
2
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diff changeset
1022 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
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1023 specified and a paired-end alignment consists of two 20-bp alignments in the
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diff changeset
1024 appropriate orientation with a 20-bp gap between them, that alignment is
c1ec08cb34f9 Uploaded
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diff changeset
1025 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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1026 be valid in that case. If trimming options `-3` or `-5` are also used, the
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1027 `-I` constraint is applied with respect to the untrimmed mates.
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1028
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1029 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
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diff changeset
1030 run. This is because larger differences bewteen `-I` and `-X` require that
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parents: 0
diff changeset
1031 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
1032 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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diff changeset
1033 efficient.
c1ec08cb34f9 Uploaded
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1034
11
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1035 Default: 0 (essentially imposing no minimum)
2
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1036
11
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diff changeset
1037 -X/--maxins <int>
2
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diff changeset
1038 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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1039 is specified and a paired-end alignment consists of two 20-bp alignments in the
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diff changeset
1040 proper orientation with a 60-bp gap between them, that alignment is considered
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diff changeset
1041 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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diff changeset
1042 that case. If trimming options `-3` or `-5` are also used, the `-X`
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1043 constraint is applied with respect to the untrimmed mates, not the trimmed
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1044 mates.
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diff changeset
1045
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diff changeset
1046 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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parents: 0
diff changeset
1047 run. This is because larger differences bewteen `-I` and `-X` require that
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parents: 0
diff changeset
1048 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
1049 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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1050 efficient.
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1051
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1052 Default: 500.
0
96d2e31a3938 Imported from capsule None
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1053
2
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1054 --fr/--rf/--ff
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1055 The upstream/downstream mate orientations for a valid paired-end alignment
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1056 against the forward reference strand. E.g., if `--fr` is specified and there is
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1057 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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1058 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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1059 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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1060 complement of mate 1 and all other constraints are met, that too is valid.
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1061 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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1062 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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1063 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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1064 for Illumina's Paired-end Sequencing Assay).
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1065
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1066 --no-mixed
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1067 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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1068 a pair, it then tries to find alignments for the individual mates. This option
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1069 disables that behavior.
0
96d2e31a3938 Imported from capsule None
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1070
2
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1071 --no-discordant
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1072 By default, `bowtie2` looks for discordant alignments if it cannot find any
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1073 concordant alignments. A discordant alignment is an alignment where both mates
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1074 align uniquely, but that does not satisfy the paired-end constraints
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1075 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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1076
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1077 --dovetail
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1078 If the mates "dovetail", that is if one mate alignment extends past the
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1079 beginning of the other such that the wrong mate begins upstream, consider that
3
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1080 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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1081
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1082 --no-contain
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1083 If one mate alignment contains the other, consider that to be non-concordant.
3
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1084 Default: a mate can contain the other in a concordant alignment.
2
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1085
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1086 --no-overlap
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1087 If one mate alignment overlaps the other at all, consider that to be
3
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diff changeset
1088 non-concordant. Default: mates can overlap in a concordant alignment.
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1089
0
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1090 ------
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1091
2
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1092 **SAM options**::
0
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1093
11
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1094 --rg-id <text>
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1095 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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1096 printed, with `<text>` as the value associated with the `ID:` tag. It also
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1097 causes the `RG:Z:` extra field to be attached to each SAM output record, with
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1098 value set to `<text>`.
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1099
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1100 --rg <text>
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1101 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
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1102 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
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1103 must also be specified. This is because the `ID` tag is required by the SAM
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1104 Specification. Specify `--rg` multiple times to set multiple fields. See the
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1105 SAM Specification for details about what fields are legal.
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1106
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1107 --omit-sec-seq
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1108 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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1109 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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1110 in those fields instead.
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1111
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1112 -----
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1113
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1114 **Other options**::
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1115
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1116 --reorder
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1117 Guarantees that output SAM records are printed in an order corresponding to the
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1118 order of the reads in the original input file, even when `-p` is set greater
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1119 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1120 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1121 not specified. Has no effect if `-p` is set to 1, since output order will
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1122 naturally correspond to input order in that case.
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1123
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1124 --seed <int>
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1125 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
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1126
2
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1127 --non-deterministic
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1128 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1129 seeds the generator with a number derived from (a) the read name, (b) the
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1130 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1131 option. This means that if two reads are identical (same name, same
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1132 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1133 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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1134 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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1135 current time. This means that Bowtie 2 will not necessarily report the same
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1136 alignment for two identical reads. This is counter-intuitive for some users,
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1137 but might be more appropriate in situations where the input consists of many
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1138 identical reads.
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1139
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1140 ]]></help>
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1141 <citations>
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1142 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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1143 <citation type="doi">10.1038/nmeth.1923</citation>
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1144 </citations>
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1145 </tool>