annotate bowtie2_wrapper.xml @ 12:781e3a3b9d31 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a326a3469adfd33babe792cf58544438582a56a1
author devteam
date Sun, 08 Jan 2017 07:58:27 -0500
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children 12450efac659
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12
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1 <tool id="bowtie2" name="Bowtie2" version="2.3.0">
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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 ## execute bowtie2
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23
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24 bowtie2
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25
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26 ## number of threads
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27 -p \${GALAXY_SLOTS:-4}
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28
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29 ## index file path
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30 -x '$index_path'
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31
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32 ## Fastq inputs
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33 #if str( $library.type ) == "single":
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34 -U '${library.input_1}'
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35 #if str( $library.unaligned_file ) == "true":
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36 --un '$output_unaligned_reads_l'
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37 #end if
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38 #if str( $library.aligned_file ) == "true":
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39 --al '$output_aligned_reads_l'
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40 #end if
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41 #elif str( $library.type ) == "paired":
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42 -1 '${library.input_1}'
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43 -2 '${library.input_2}'
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44 #if str( $library.paired_options.paired_options_selector ) == "yes":
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45 -I "${library.paired_options.I}"
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46 -X "${library.paired_options.X}"
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47 ${library.paired_options.fr_rf_ff}
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48 ${library.paired_options.no_mixed}
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49 ${library.paired_options.no_discordant}
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50 ${library.paired_options.dovetail}
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51 ${library.paired_options.no_contain}
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52 ${library.paired_options.no_overlap}
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53 #end if
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54 #if str( $library.unaligned_file ) == "true":
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55 --un-conc $output_unaligned_reads_l
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56 #end if
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57 #if str( $library.aligned_file ) == "true":
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58 --al-conc $output_aligned_reads_l
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59 #end if
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60 #else
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61 ## prepare collection
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62 -1 $library.input_1.forward
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63 -2 $library.input_1.reverse
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64 #if str( $library.paired_options.paired_options_selector ) == "yes":
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65 -I "${library.paired_options.I}"
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66 -X "${library.paired_options.X}"
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67 ${library.paired_options.fr_rf_ff}
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68 ${library.paired_options.no_mixed}
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69 ${library.paired_options.no_discordant}
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70 ${library.paired_options.dovetail}
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71 ${library.paired_options.no_contain}
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72 ${library.paired_options.no_overlap}
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73 #end if
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74 #if str( $library.unaligned_file ) == "true":
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75 --un-conc '$output_unaligned_reads_l'
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76 #end if
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77 #end if
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78
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79 ## Read group information.
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80 @define_read_group_helpers@
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81 #if str( $library.type ) == "single":
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82 #set $rg_auto_name = $read_group_name_default($library.input_1)
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83 #elif str( $library.type ) == "paired":
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84 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2)
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85 #else
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86 #set $rg_auto_name = $read_group_name_default($library.input_1)
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87 #end if
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88 @set_use_rg_var@
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89 @set_read_group_vars@
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90 #if $use_rg
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91 $format_read_group("", $rg_id, '"', arg='--rg-id ')
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92 $format_read_group("SM:", $rg_sm, '"', arg='--rg ')
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93 $format_read_group("PL:", $rg_pl, '"', arg='--rg ')
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94 $format_read_group("LB:", $rg_lb, '"', arg='--rg ')
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95 $format_read_group("CN:", $rg_cn, '"', arg='--rg ')
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96 $format_read_group("DS:", $rg_ds, '"', arg='--rg ')
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97 $format_read_group("DT:", $rg_dt, '"', arg='--rg ')
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98 $format_read_group("FO:", $rg_fo, '"', arg='--rg ')
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99 $format_read_group("KS:", $rg_ks, '"', arg='--rg ')
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100 $format_read_group("PG:", $rg_pg, '"', arg='--rg ')
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101 $format_read_group("PI:", $rg_pi, '"', arg='--rg ')
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102 $format_read_group("PU:", $rg_pu, '"', arg='--rg ')
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103 #end if
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104
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105 ## Analysis type
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106 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ):
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107 $analysis_type.presets
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108 #elif str( $analysis_type.analysis_type_selector ) == "full":
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109 #if str( $analysis_type.input_options.input_options_selector ) == "yes":
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110 --skip "${analysis_type.input_options.skip}"
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111 --qupto "${analysis_type.input_options.qupto}"
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112 --trim5 "${analysis_type.input_options.trim5}"
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113 --trim3 "${analysis_type.input_options.trim3}"
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114 ${analysis_type.input_options.qv_encoding}
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115 ${analysis_type.input_options.solexa_quals}
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116 ${analysis_type.input_options.int_quals}
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117 #end if
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118
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119 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes":
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120 -N "${analysis_type.alignment_options.N}"
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121 -L "${analysis_type.alignment_options.L}"
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122 -i "${analysis_type.alignment_options.i}"
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123 --n-ceil "${analysis_type.alignment_options.n_ceil}"
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124 --dpad "${analysis_type.alignment_options.dpad}"
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125 --gbar "${analysis_type.alignment_options.gbar}"
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126 ${analysis_type.alignment_options.ignore_quals}
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127 ${analysis_type.alignment_options.nofw}
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128 ${analysis_type.alignment_options.norc}
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129 ${analysis_type.alignment_options.no_1mm_upfront}
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130 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end":
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131 --end-to-end
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132 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}"
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133 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local":
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134 --local
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135 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}"
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136 #end if
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137 #end if
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138
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139 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes":
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140 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ):
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141 --ma "${analysis_type.scoring_options.ma}"
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142 #end if
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143 --mp "${analysis_type.scoring_options.mp}"
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144 --np "${analysis_type.scoring_options.np}"
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145 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}"
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146 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}"
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147 #end if
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148
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149 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k":
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150 -k "${analysis_type.reporting_options.k}"
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151 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a":
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152 -a
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153 #end if
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154
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155 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes":
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156 -D "${analysis_type.effort_options.D}"
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157 -R "${analysis_type.effort_options.R}"
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158 #end if
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159
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160 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
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161 ${analysis_type.sam_options.no_unal}
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162 ${analysis_type.sam_options.omit_sec_seq}
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163 #end if
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164
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165 #if str( $analysis_type.other_options.other_options_selector ) == "yes":
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166 ${analysis_type.other_options.reorder}
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167 ${analysis_type.other_options.non_deterministic}
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168 --seed "${analysis_type.other_options.seed}"
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169 #end if
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170
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171 #elif str( $analysis_type.analysis_type_selector ) == "cline":
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172 ${analysis_type.cline}
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173 #end if
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174
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175 ## mapping stats (i.e. stderr from bowtie2)
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176 #if $save_mapping_stats
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177 2> '$mapping_stats'
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178 #end if
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179
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180 ## output file
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181 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ):
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182 | samtools sort -O bam -o '$output'
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183 #else
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184 > '$output_sam'
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185 #end if
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186
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187 ## rename unaligned sequence files
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188 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
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189 #from os.path import splitext
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190 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
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191 && mv "${ _unaligned_root }.1${_unaligned_ext}" '$output_unaligned_reads_l'
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192 && mv "${ _unaligned_root }.2${_unaligned_ext}" '$output_unaligned_reads_r'
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193 #end if
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194 #if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
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195 #from os.path import splitext
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196 #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
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197 && mv "${ _aligned_root }.1${_aligned_ext}" '$output_aligned_reads_l'
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198 && mv "${ _aligned_root }.2${_aligned_ext}" '$output_aligned_reads_r'
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199 #end if
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200
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201 ]]></command>
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202 <inputs>
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203 <!-- single/paired -->
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204 <conditional name="library">
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205 <param name="type" type="select" label="Is this single or paired library">
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206 <option value="single">Single-end</option>
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207 <option value="paired">Paired-end</option>
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208 <option value="paired_collection">Paired-end Dataset Collection</option>
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209 </param>
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210
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211 <when value="single">
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212 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
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213 <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; This triggers --un parameter for single reads and --un-conc for paired reads" />
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214 <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; This triggers --al parameter for single reads and --al-conc for paired reads" />
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215 </when>
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216 <when value="paired">
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217 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
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218 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
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219 <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; This triggers --un parameter for single reads and --un-conc for paired reads" />
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220 <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; This triggers --al parameter for single reads and --al-conc for paired reads" />
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221 <conditional name="paired_options">
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222 <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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223 <option value="no" selected="True">No</option>
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224 <option value="yes">Yes</option>
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225 </param>
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226 <when value="yes">
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227 <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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228 <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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229 <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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230 <option value="--fr" selected="True">--fr</option>
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231 <option value="--rf">--rf</option>
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232 <option value="--ff">--ff</option>
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233 </param>
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234 <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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235 <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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236 <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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237 <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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238 <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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239 </when>
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240 <when value="no">
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241 <!-- do nothing -->
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242 </when>
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243 </conditional>
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244 </when>
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245 <when value="paired_collection">
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246 <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype &quot;fastqsanger&quot;" />
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247 <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; This triggers --un parameter for single reads and --un-conc for paired reads" />
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248 <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; This triggers --al parameter for single reads and --al-conc for paired reads" />
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249 <conditional name="paired_options">
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250 <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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251 <option value="no" selected="True">No</option>
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252 <option value="yes">Yes</option>
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253 </param>
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254 <when value="yes">
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255 <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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256 <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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257 <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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258 <option value="--fr" selected="True">--fr</option>
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259 <option value="--rf">--rf</option>
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260 <option value="--ff">--ff</option>
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261 </param>
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262 <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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263 <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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264 <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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265 <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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266 <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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267 </when>
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268 <when value="no">
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269 <!-- do nothing -->
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270 </when>
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271 </conditional>
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272 </when>
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273 </conditional>
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274
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275 <!-- reference genome -->
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276 <conditional name="reference_genome">
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277 <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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278 <option value="indexed">Use a built-in genome index</option>
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279 <option value="history">Use a genome from the history and build index</option>
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280 </param>
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281 <when value="indexed">
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282 <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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283 <options from_data_table="bowtie2_indexes">
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284 <filter type="sort_by" column="2"/>
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285 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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286 </options>
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287 </param>
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288 </when>
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289 <when value="history">
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290 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
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291 </when>
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292 </conditional>
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293
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294 <!-- read group settings -->
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295 <expand macro="read_group_conditional" />
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296 <conditional name="analysis_type">
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297 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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298 <option value="simple">1: Default setting only</option>
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299 <option value="full">2: Full parameter list</option>
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300 </param>
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301 <when value="simple">
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302 <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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303 <option value="no_presets" selected="True">No, just use defaults</option>
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304 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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305 <option value="--fast">Fast end-to-end (--fast)</option>
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306 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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307 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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308 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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309 <option value="--fast-local">Fast local (--fast-local)</option>
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310 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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311 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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312 </param>
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313 </when>
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314 <when value="full">
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315 <conditional name="input_options">
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316 <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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317 <option value="yes">Yes</option>
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318 <option value="no" selected="true">No</option>
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319 </param>
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320 <when value="yes">
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321 <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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322 <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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323 <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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324 <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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325 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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326 <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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327 <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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328 </param>
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329 <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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330 <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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331 </when>
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332 <when value="no">
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333 <!-- do nothing -->
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334 </when>
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335 </conditional>
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336 <conditional name="alignment_options">
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337 <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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338 <option value="yes">Yes</option>
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339 <option value="no" selected="true">No</option>
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340 </param>
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341 <when value="yes">
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342 <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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343 <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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344 <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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345 <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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346 <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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347 <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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348 <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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349 <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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350 <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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351 <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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352 <conditional name="align_mode">
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353 <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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354 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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355 <option value="local">Local (--local)</option>
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356 </param>
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357 <when value="end-to-end">
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358 <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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359 </when>
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360 <when value="local">
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361 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/>
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362 </when>
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363 </conditional>
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364 </when>
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365 <when value="no">
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366 <!-- do nothing -->
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367 </when>
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368 </conditional>
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369 <conditional name="scoring_options">
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370 <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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371 <option value="yes">Yes</option>
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372 <option value="no" selected="true">No</option>
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373 </param>
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374 <when value="yes">
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375 <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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376 <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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377 <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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378 <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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379 <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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380 <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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381 <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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382 </when>
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383 <when value="no">
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384 <!-- do nothing -->
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385 </when>
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386 </conditional>
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387 <conditional name="reporting_options">
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388 <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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389 <option value="no" selected="true">No, do not set</option>
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390 <option value="k">Set -k option and enter -k value</option>
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391 <option value="a">Set -a option</option>
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392 </param>
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393 <when value="no">
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394 <!-- do nothing -->
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395 </when>
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396 <when value="k">
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397 <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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398 </when>
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399 <when value="a">
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400 <!-- do nothing here; set -a flag on the command line-->
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401 </when>
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402 </conditional>
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403 <conditional name="effort_options">
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404 <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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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="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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410 <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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411 </when>
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412 <when value="no">
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413 <!-- do nothing -->
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414 </when>
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415 </conditional>
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416
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417 <conditional name="sam_options">
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418 <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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419 <option value="yes">Yes</option>
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420 <option value="no" selected="true">No</option>
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421 </param>
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422 <when value="yes">
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423 <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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424 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
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425 </when>
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426 <when value="no">
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427 <!-- do nothing -->
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428 </when>
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429 </conditional>
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430 <conditional name="other_options">
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431 <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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432 <option value="yes">Yes</option>
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433 <option value="no" selected="true">No</option>
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434 </param>
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435 <when value="yes">
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436 <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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437 <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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438 <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"/>
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439 </when>
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440 <when value="no">
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441 <!-- do nothing -->
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442 </when>
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443 </conditional>
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444 <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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445 </when>
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446 </conditional>
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447 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
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448 </inputs>
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449
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450 <!-- define outputs -->
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451
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452 <outputs>
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453
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454 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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455 <filter>library['unaligned_file'] is True</filter>
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456 <actions>
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457 <conditional name="library.type">
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458 <when value="single">
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459 <action type="format">
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460 <option type="from_param" name="library.input_1" param_attribute="ext" />
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461 </action>
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462 </when>
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463 <when value="paired">
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464 <action type="format">
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465 <option type="from_param" name="library.input_1" param_attribute="ext" />
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466 </action>
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467 </when>
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468 <when value="paired_collection">
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469 <action type="format">
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470 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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471 </action>
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472 </when>
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473 </conditional>
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474 </actions>
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475 </data>
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476 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
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477 <filter>library['aligned_file'] is True</filter>
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478 <actions>
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479 <conditional name="library.type">
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diff changeset
480 <when value="single">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
481 <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
482 <option type="from_param" name="library.input_1" 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
483 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
484 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
485 <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
486 <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
487 <option type="from_param" name="library.input_1" 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
488 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
489 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
490 <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
491 <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
492 <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
493 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
494 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
495 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
496 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
497 </data>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
498 <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
499 <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
500 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
501 <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
502 <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
503 <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
504 <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
505 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
506 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
507 <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
508 <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
509 <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
510 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
511 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
512 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
513 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
514 </data>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
515 <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
516 <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
517 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
518 <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
519 <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
520 <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
521 <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
522 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
523 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
524 <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
525 <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
526 <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
527 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
528 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
529 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
530 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
531 </data>
11
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
devteam
parents: 10
diff changeset
532
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
533 <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
534 <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
535 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
536 <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
537 <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
538 <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
539 <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
devteam
parents: 6
diff changeset
540 <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
devteam
parents: 6
diff changeset
541 <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
devteam
parents: 6
diff changeset
542 </option>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
543 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
544 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
545 <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
546 <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
547 <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
548 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
549 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
550 </conditional>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
551 </actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
552 </data>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
553
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
554 <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
555 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
556 <actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
557 <conditional name="reference_genome.source">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
558 <when value="indexed">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
559 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
560 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
561 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
562 <filter type="param_value" ref="reference_genome.index" column="0"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
563 </option>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
564 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
565 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
566 <when value="history">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
567 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
568 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
569 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
570 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
571 </conditional>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
572 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
573 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
574 <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
devteam
parents: 8
diff changeset
575 <filter>save_mapping_stats 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
576 </data>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
577
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
578 </outputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
579
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
580 <tests>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
581 <test>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
582 <!-- basic test on single paired default run -->
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
583 <param name="type" value="paired"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
584 <param name="selection" value="no"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
585 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
586 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
587 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
588 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
589 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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590 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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591 <param name="own_file" value="bowtie2-ref.fasta" />
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592 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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593 </test>
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594 <test>
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595 <!-- basic test on single paired default run -->
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596 <param name="type" value="paired"/>
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597 <param name="selection" value="no"/>
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598 <param name="paired_options_selector" value="no"/>
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599 <param name="unaligned_file" value="false"/>
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600 <param name="analysis_type_selector" value="simple"/>
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601 <param name="rg_selector" value="set"/>
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602 <param name="ID" value="rg1"/>
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603 <param name="PL" value="CAPILLARY"/>
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604 <param name="source" value="history" />
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605 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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606 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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607 <param name="own_file" value="bowtie2-ref.fasta" />
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608 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
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609 </test>
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610 <test>
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611 <!-- basic test on single paired default run with stats-->
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612 <param name="type" value="paired"/>
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613 <param name="selection" value="no"/>
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614 <param name="paired_options_selector" value="no"/>
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615 <param name="unaligned_file" value="false"/>
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616 <param name="analysis_type_selector" value="simple"/>
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617 <param name="source" value="history" />
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618 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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619 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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620 <param name="own_file" value="bowtie2-ref.fasta" />
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621 <param name="save_mapping_stats" value="true" />
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622 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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623 <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
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624 </test>
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625 </tests>
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626
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627 <help><![CDATA[
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628
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629 **Bowtie2 Overview**
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630
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631 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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632 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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633
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634 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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635 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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636 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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637
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638 -----
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639
2
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640 **Selecting reference genomes for Bowtie2**
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641
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642 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:
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643
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644 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.
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645 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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646
2
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647 If your genome of interest is not listed here you have two choices:
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648
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649 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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650 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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651
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652 ------
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653
2
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654 .. class:: infomark
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655
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656 **Bowtie2 options**
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657
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658 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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659
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660 -----
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661
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662 **Inputs**
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663
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664 Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files.
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665
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666 ------
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667
2
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668 **Input options**::
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669
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670 -s/--skip <int>
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671 Skip (i.e. do not align) the first `<int>` reads or pairs in the input.
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672
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673 -u/--qupto <int>
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674 Align the first `<int>` reads or read pairs from the input (after the
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675 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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676
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677 -5/--trim5 <int>
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678 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0).
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679
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680 -3/--trim3 <int>
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681 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0).
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682
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683 --phred33
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684 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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685 also called the "Phred+33" encoding, which is used by the very latest Illumina
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686 pipelines.
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687
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688 --phred64
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689 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
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690 also called the "Phred+64" encoding.
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691
2
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692 --solexa-quals
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693 Convert input qualities from Solexa Phred quality (which can be negative) to
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694 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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695 Pipeline versions (prior to 1.3). Default: off.
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696
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697 --int-quals
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698 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`....
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699 Integers are treated as being on the Phred quality scale unless
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700 `--solexa-quals` is also specified. Default: off.
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701
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702 ------
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703
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704 **Presets in `--end-to-end` mode**::
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705
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706 --very-fast
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707 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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708
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709 --fast
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710 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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711
2
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712 --sensitive
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713 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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714
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715 --very-sensitive
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716 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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diff changeset
717
96d2e31a3938 Imported from capsule None
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718 ------
96d2e31a3938 Imported from capsule None
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719
2
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diff changeset
720 **Presets options in `--local` mode**::
0
96d2e31a3938 Imported from capsule None
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parents:
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721
2
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parents: 0
diff changeset
722 --very-fast-local
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parents: 0
diff changeset
723 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
724
2
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parents: 0
diff changeset
725 --fast-local
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parents: 0
diff changeset
726 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
727
2
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parents: 0
diff changeset
728 --sensitive-local
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parents: 0
diff changeset
729 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
96d2e31a3938 Imported from capsule None
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parents:
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730
2
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parents: 0
diff changeset
731 --very-sensitive-local
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parents: 0
diff changeset
732 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
11
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diff changeset
733
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
734 ------
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
735
2
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parents: 0
diff changeset
736 **Alignment options**::
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parents: 0
diff changeset
737
11
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parents: 10
diff changeset
738 -N <int>
3
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parents: 2
diff changeset
739 Sets the number of mismatches to allowed in a seed alignment during multiseed
ceb6467e276c Uploaded
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parents: 2
diff changeset
740 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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parents: 0
diff changeset
741 (often much slower) but increases sensitivity. Default: 0.
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parents: 0
diff changeset
742
11
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parents: 10
diff changeset
743 -L <int>
3
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parents: 2
diff changeset
744 Sets the length of the seed substrings to align during multiseed alignment.
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parents: 2
diff changeset
745 Smaller values make alignment slower but more sensitive. Default: the
ceb6467e276c Uploaded
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diff changeset
746 `--sensitive` preset is used by default, which sets `-L` to 22 in
ceb6467e276c Uploaded
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parents: 2
diff changeset
747 `--end-to-end` mode and to 20 in `--local` mode.
2
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parents: 0
diff changeset
748
11
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parents: 10
diff changeset
749 -i <func>
2
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diff changeset
750 Sets a function governing the interval between seed substrings to use during
3
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diff changeset
751 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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parents: 0
diff changeset
752 length is 10, and the seed interval is 6, the seeds extracted will be:
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diff changeset
753
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diff changeset
754 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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diff changeset
755 Seed 1 fw: TAGCTACGCT
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diff changeset
756 Seed 1 rc: AGCGTAGCTA
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diff changeset
757 Seed 2 fw: CGCTCTACGC
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diff changeset
758 Seed 2 rc: GCGTAGAGCG
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759 Seed 3 fw: ACGCTATCAT
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760 Seed 3 rc: ATGATAGCGT
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761 Seed 4 fw: TCATGCATAA
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762 Seed 4 rc: TTATGCATGA
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763
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764 Since it's best to use longer intervals for longer reads, this parameter sets
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765 the interval as a function of the read length, rather than a single
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diff changeset
766 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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parents: 0
diff changeset
767 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length.
3
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parents: 2
diff changeset
768 If the function returns a result less than
2
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diff changeset
769 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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diff changeset
770 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75`
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parents: 0
diff changeset
771 in `--local` mode.
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diff changeset
772
11
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parents: 10
diff changeset
773 --n-ceil <func>
2
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diff changeset
774 Sets a function governing the maximum number of ambiguous characters (usually
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diff changeset
775 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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parents: 0
diff changeset
776 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
3
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parents: 2
diff changeset
777 where x is the read length. Reads exceeding this ceiling are filtered out.
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diff changeset
778 Default: `L,0,0.15`.
2
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parents: 0
diff changeset
779
11
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parents: 10
diff changeset
780 --dpad <int>
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diff changeset
781 "Pads" dynamic programming problems by `<int>` columns on either side to allow
2
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diff changeset
782 gaps. Default: 15.
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diff changeset
783
11
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parents: 10
diff changeset
784 --gbar <int>
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diff changeset
785 Disallow gaps within `<int>` positions of the beginning or end of the read.
2
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diff changeset
786 Default: 4.
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787
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788 --ignore-quals
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diff changeset
789 When calculating a mismatch penalty, always consider the quality value at the
11
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790 mismatched position to be the highest possible, regardless of the actual value.
2
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791 I.e. input is treated as though all quality values are high. This is also the
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diff changeset
792 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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793 `-r`, or `-c` modes).
0
96d2e31a3938 Imported from capsule None
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794
2
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795 --nofw/--norc
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diff changeset
796 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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diff changeset
797 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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798 not attempt to align unpaired reads against the reverse-complement (Crick)
c1ec08cb34f9 Uploaded
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diff changeset
799 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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diff changeset
800 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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diff changeset
801 paired-end configurations corresponding to fragments from the reverse-complement
11
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diff changeset
802 (Crick) strand. Default: both strands enabled.
2
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diff changeset
803
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diff changeset
804 --no-1mm-upfront
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diff changeset
805 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
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diff changeset
806 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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diff changeset
807 alignments can be found very quickly, and many short read alignments have exact or
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808 near-exact end-to-end alignments. However, this can lead to unexpected
3
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diff changeset
809 alignments when the user also sets options governing the multiseed heuristic,
2
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810 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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diff changeset
811 to the length of the read, the user will be surprised to find 1-mismatch alignments
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812 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
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813 alignments before using the multiseed heuristic, which leads to the expected
2
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diff changeset
814 behavior when combined with options such as `-L` and `-N`. This comes at the
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diff changeset
815 expense of speed.
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816
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817 --end-to-end
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818 In this mode, Bowtie 2 requires that the entire read align from one end to the
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diff changeset
819 other, without any trimming (or "soft clipping") of characters from either end.
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diff changeset
820 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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821 are less than or equal to 0, and the greatest possible alignment score is 0.
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diff changeset
822 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
96d2e31a3938 Imported from capsule None
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823
2
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824 --local
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825 In this mode, Bowtie 2 does not require that the entire read align from one end
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diff changeset
826 to the other. Rather, some characters may be omitted ("soft clipped") from the
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diff changeset
827 ends in order to achieve the greatest possible alignment score. The match bonus
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828 `--ma` is used in this mode, and the best possible alignment score is equal to
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diff changeset
829 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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diff changeset
830 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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diff changeset
831 the local version of the preset (`--very-fast-local`). This is mutually
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diff changeset
832 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
11
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833
2
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834 -----
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835
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diff changeset
836 **Scoring options**::
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diff changeset
837
11
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diff changeset
838 --ma <int>
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diff changeset
839 Sets the match bonus. In `--local` mode `<int>` is added to the alignment
2
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840 score for each position where a read character aligns to a reference character
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diff changeset
841 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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842
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843 --mp MX,MN
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diff changeset
844 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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diff changeset
845 number less than or equal to `MX` and greater than or equal to `MN` is
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diff changeset
846 subtracted from the alignment score for each position where a read character
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diff changeset
847 aligns to a reference character, the characters do not match, and neither is an
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diff changeset
848 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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diff changeset
849 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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850 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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diff changeset
851
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diff changeset
852 --np <int>
2
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diff changeset
853 Sets penalty for positions where the read, reference, or both, contain an
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diff changeset
854 ambiguous character such as `N`. Default: 1.
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diff changeset
855
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diff changeset
856 --rdg <int1>,<int2>
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parents: 10
diff changeset
857 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of
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diff changeset
858 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3.
2
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parents: 0
diff changeset
859
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diff changeset
860 --rfg <int1>,<int2>
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diff changeset
861 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
862 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default:
2
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diff changeset
863 5, 3.
0
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parents:
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864
11
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diff changeset
865 --score-min <func>
2
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diff changeset
866 Sets a function governing the minimum alignment score needed for an alignment to
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867 be considered "valid" (i.e. good enough to report). This is a function of read
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868 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
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diff changeset
869 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
870 the default in `--local` mode is `G,20,8`.
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parents: 10
diff changeset
871
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872 -----
2
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diff changeset
873
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diff changeset
874 **Reporting options**::
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diff changeset
875
11
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diff changeset
876 -k <int>
2
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diff changeset
877 By default, `bowtie2` searches for distinct, valid alignments for each read.
c1ec08cb34f9 Uploaded
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diff changeset
878 When it finds a valid alignment, it continues looking for alignments that are
c1ec08cb34f9 Uploaded
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diff changeset
879 nearly as good or better. The best alignment found is reported (randomly
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
880 selected from among best if tied). Information about the best alignments is
c1ec08cb34f9 Uploaded
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diff changeset
881 used to estimate mapping quality and to set SAM optional fields, such as
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diff changeset
882 `AS:i` and `XS:i`.
c1ec08cb34f9 Uploaded
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diff changeset
883
c1ec08cb34f9 Uploaded
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diff changeset
884 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
11
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diff changeset
885 searches for at most `<int>` distinct, valid alignments for each read. The
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
886 search terminates when it can't find more distinct valid alignments, or when it
11
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parents: 10
diff changeset
887 finds `<int>`, whichever happens first. All alignments found are reported in
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
888 descending order by alignment score. The alignment score for a paired-end
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
889 alignment equals the sum of the alignment scores of the individual mates. Each
c1ec08cb34f9 Uploaded
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diff changeset
890 reported read or pair alignment beyond the first has the SAM 'secondary' bit
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
891 (which equals 256) set in its FLAGS field. For reads that have more than
11
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parents: 10
diff changeset
892 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the
b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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diff changeset
893 `<int>` alignments reported are the best possible in terms of alignment score.
2
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diff changeset
894 `-k` is mutually exclusive with `-a`.
0
96d2e31a3938 Imported from capsule None
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parents:
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895
2
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diff changeset
896 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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diff changeset
897 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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diff changeset
898
c1ec08cb34f9 Uploaded
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diff changeset
899 -a
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diff changeset
900 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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901 is mutually exclusive with `-k`.
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902
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903 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
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diff changeset
904 aligning reads to long, repetitive genomes this mode can be very, very slow.
11
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diff changeset
905
2
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diff changeset
906 -----
c1ec08cb34f9 Uploaded
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diff changeset
907
c1ec08cb34f9 Uploaded
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diff changeset
908 **Effort options**::
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diff changeset
909
11
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diff changeset
910 -D <int>
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diff changeset
911 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2
2
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912 moves on, using the alignments found so far. A seed extension "fails" if it
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913 does not yield a new best or a new second-best alignment. This limit is
c1ec08cb34f9 Uploaded
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914 automatically adjusted up when -k or -a are specified. Default: 15.
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915
11
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diff changeset
916 -R <int>
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diff changeset
917 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with
2
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918 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
c1ec08cb34f9 Uploaded
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919 (same length, same number of mismatches allowed) at different offsets and
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parents: 0
diff changeset
920 searches for more alignments. A read is considered to have repetitive seeds if
c1ec08cb34f9 Uploaded
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diff changeset
921 the total number of seed hits divided by the number of seeds that aligned at
c1ec08cb34f9 Uploaded
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diff changeset
922 least once is greater than 300. Default: 2.
11
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diff changeset
923
2
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diff changeset
924 -----
c1ec08cb34f9 Uploaded
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925
c1ec08cb34f9 Uploaded
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926 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
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parents:
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927
11
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diff changeset
928 -I/--minins <int>
2
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parents: 0
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929 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
c1ec08cb34f9 Uploaded
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parents: 0
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930 specified and a paired-end alignment consists of two 20-bp alignments in the
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
931 appropriate orientation with a 20-bp gap between them, that alignment is
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
932 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
c1ec08cb34f9 Uploaded
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933 be valid in that case. If trimming options `-3` or `-5` are also used, the
c1ec08cb34f9 Uploaded
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934 `-I` constraint is applied with respect to the untrimmed mates.
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parents: 0
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935
c1ec08cb34f9 Uploaded
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diff changeset
936 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
937 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
938 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
939 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
940 efficient.
c1ec08cb34f9 Uploaded
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941
11
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942 Default: 0 (essentially imposing no minimum)
2
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943
11
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diff changeset
944 -X/--maxins <int>
2
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diff changeset
945 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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946 is specified and a paired-end alignment consists of two 20-bp alignments in the
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947 proper orientation with a 60-bp gap between them, that alignment is considered
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diff changeset
948 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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diff changeset
949 that case. If trimming options `-3` or `-5` are also used, the `-X`
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950 constraint is applied with respect to the untrimmed mates, not the trimmed
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951 mates.
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952
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953 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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diff changeset
954 run. This is because larger differences bewteen `-I` and `-X` require that
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
955 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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parents: 0
diff changeset
956 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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957 efficient.
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958
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959 Default: 500.
0
96d2e31a3938 Imported from capsule None
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960
2
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961 --fr/--rf/--ff
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962 The upstream/downstream mate orientations for a valid paired-end alignment
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963 against the forward reference strand. E.g., if `--fr` is specified and there is
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diff changeset
964 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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965 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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966 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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967 complement of mate 1 and all other constraints are met, that too is valid.
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968 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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969 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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970 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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971 for Illumina's Paired-end Sequencing Assay).
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972
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973 --no-mixed
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974 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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975 a pair, it then tries to find alignments for the individual mates. This option
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976 disables that behavior.
0
96d2e31a3938 Imported from capsule None
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977
2
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978 --no-discordant
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979 By default, `bowtie2` looks for discordant alignments if it cannot find any
c1ec08cb34f9 Uploaded
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980 concordant alignments. A discordant alignment is an alignment where both mates
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981 align uniquely, but that does not satisfy the paired-end constraints
c1ec08cb34f9 Uploaded
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982 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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983
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984 --dovetail
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985 If the mates "dovetail", that is if one mate alignment extends past the
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diff changeset
986 beginning of the other such that the wrong mate begins upstream, consider that
3
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987 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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988
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989 --no-contain
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990 If one mate alignment contains the other, consider that to be non-concordant.
3
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991 Default: a mate can contain the other in a concordant alignment.
2
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992
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993 --no-overlap
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994 If one mate alignment overlaps the other at all, consider that to be
3
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diff changeset
995 non-concordant. Default: mates can overlap in a concordant alignment.
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996
0
96d2e31a3938 Imported from capsule None
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997 ------
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998
2
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diff changeset
999 **SAM options**::
0
96d2e31a3938 Imported from capsule None
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1000
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1001 --rg-id <text>
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diff changeset
1002 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be
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1003 printed, with `<text>` as the value associated with the `ID:` tag. It also
2
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1004 causes the `RG:Z:` extra field to be attached to each SAM output record, with
11
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1005 value set to `<text>`.
0
96d2e31a3938 Imported from capsule None
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1006
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1007 --rg <text>
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1008 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
2
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diff changeset
1009 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
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1010 must also be specified. This is because the `ID` tag is required by the SAM
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1011 Specification. Specify `--rg` multiple times to set multiple fields. See the
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1012 SAM Specification for details about what fields are legal.
0
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1013
2
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1014 --omit-sec-seq
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diff changeset
1015 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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1016 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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diff changeset
1017 in those fields instead.
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1018
2
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1019 -----
0
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1020
2
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1021 **Other options**::
0
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1022
2
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1023 --reorder
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diff changeset
1024 Guarantees that output SAM records are printed in an order corresponding to the
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diff changeset
1025 order of the reads in the original input file, even when `-p` is set greater
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diff changeset
1026 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1027 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1028 not specified. Has no effect if `-p` is set to 1, since output order will
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1029 naturally correspond to input order in that case.
0
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1030
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diff changeset
1031 --seed <int>
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1032 Use `<int>` as the seed for pseudo-random number generator. Default: 0.
0
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1033
2
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1034 --non-deterministic
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1035 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1036 seeds the generator with a number derived from (a) the read name, (b) the
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1037 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1038 option. This means that if two reads are identical (same name, same
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1039 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1040 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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1041 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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1042 current time. This means that Bowtie 2 will not necessarily report the same
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1043 alignment for two identical reads. This is counter-intuitive for some users,
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1044 but might be more appropriate in situations where the input consists of many
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1045 identical reads.
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1046
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b4e9cf5f2ae8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e857ba2691ca15b6239890baf98dbe7bc3ccbd
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1047 ]]></help>
2
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1048 <citations>
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1049 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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1050 <citation type="doi">10.1038/nmeth.1923</citation>
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1051 </citations>
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1052 </tool>