Mercurial > repos > devteam > bowtie2

annotate bowtie2_wrapper.xml @ 10:a9d4f71dbfb0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
author devteam
date Tue, 22 Mar 2016 14:58:55 -0400
parents 82414e16b6bd
children b4e9cf5f2ae8
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1 <tool id="bowtie2" name="Bowtie2" version="2.2.6.2">
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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 <version_command>bowtie2 --version</version_command>
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7 <requirements>
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8 <requirement type="package" version="2.2.6">bowtie2</requirement>
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9 <requirement type="package" version="1.2">samtools</requirement>
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10 </requirements>
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11 <command>
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12 ## prepare bowtie2 index
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13 #set index_path = ''
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14 #if str($reference_genome.source) == "history":
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15 bowtie2-build "$reference_genome.own_file" genome &amp;&amp;
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16 ln -s "$reference_genome.own_file" genome.fa &amp;&amp;
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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 $save_mapping_stats
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177 2&gt; "$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 view -Su - | samtools sort -o - - &gt; $output
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183 #else
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184 &gt; $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( $output_unaligned_reads_l ) )
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191 &amp;&amp; mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }"
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192 &amp;&amp; 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( $output_aligned_reads_l ) )
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197 &amp;&amp; mv "${ _aligned_root }.1${_aligned_ext}" "${ output_aligned_reads_l }"
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198 &amp;&amp; mv "${ _aligned_root }.2${_aligned_ext}" "${ output_aligned_reads_r }"
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199 #end if
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200
0
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201 </command>
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202 <!-- basic error handling -->
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203 <stdio>
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204 <exit_code range="1:" level="fatal" description="Tool exception" />
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205 </stdio>
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206
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207 <inputs>
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208 <!-- single/paired -->
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209 <conditional name="library">
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210 <param name="type" type="select" label="Is this single or paired library">
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211 <option value="single">Single-end</option>
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212 <option value="paired">Paired-end</option>
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213 <option value="paired_collection">Paired-end Dataset Collection</option>
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214 </param>
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215
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216 <when value="single">
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217 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
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218 <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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219 <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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220 </when>
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221 <when value="paired">
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222 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
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223 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
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224 <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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225 <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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226 <conditional name="paired_options">
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227 <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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228 <option value="no" selected="True">No</option>
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229 <option value="yes">Yes</option>
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230 </param>
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231 <when value="yes">
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232 <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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233 <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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234 <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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235 <option value="--fr" selected="True">--fr</option>
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236 <option value="--rf">--rf</option>
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237 <option value="--ff">--ff</option>
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238 </param>
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239 <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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240 <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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241 <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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242 <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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243 <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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244 </when>
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245 <when value="no">
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246 <!-- do nothing -->
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247 </when>
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248 </conditional>
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249 </when>
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250 <when value="paired_collection">
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251 <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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252 <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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253 <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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254 <conditional name="paired_options">
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255 <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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256 <option value="no" selected="True">No</option>
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257 <option value="yes">Yes</option>
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258 </param>
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259 <when value="yes">
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260 <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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261 <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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262 <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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263 <option value="--fr" selected="True">--fr</option>
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264 <option value="--rf">--rf</option>
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265 <option value="--ff">--ff</option>
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266 </param>
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267 <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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268 <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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269 <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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270 <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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271 <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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272 </when>
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273 <when value="no">
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274 <!-- do nothing -->
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275 </when>
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276 </conditional>
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277 </when>
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278 </conditional>
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279
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280 <!-- reference genome -->
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281 <conditional name="reference_genome">
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282 <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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283 <option value="indexed">Use a built-in genome index</option>
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284 <option value="history">Use a genome from the history and build index</option>
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285 </param>
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286 <when value="indexed">
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287 <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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288 <options from_data_table="bowtie2_indexes">
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289 <filter type="sort_by" column="2"/>
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290 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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291 </options>
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292 </param>
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293 </when>
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294 <when value="history">
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295 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />
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296 </when>
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297 </conditional>
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298
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299 <!-- read group settings -->
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300 <expand macro="read_group_conditional" />
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301 <conditional name="analysis_type">
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302 <param name="analysis_type_selector" type="select" label="Select analysis mode">
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303 <option value="simple">1: Default setting only</option>
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304 <option value="full">2: Full parameter list</option>
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305 </param>
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306 <when value="simple">
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307 <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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308 <option value="no_presets" selected="True">No, just use defaults</option>
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309 <option value="--very-fast">Very fast end-to-end (--very-fast)</option>
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310 <option value="--fast">Fast end-to-end (--fast)</option>
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311 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option>
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312 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option>
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313 <option value="--very-fast-local">Very fast local (--very-fast-local)</option>
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314 <option value="--fast-local">Fast local (--fast-local)</option>
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315 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option>
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316 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option>
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317 </param>
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318 </when>
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319 <when value="full">
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320 <conditional name="input_options">
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321 <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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322 <option value="yes">Yes</option>
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323 <option value="no" selected="true">No</option>
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324 </param>
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325 <when value="yes">
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326 <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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327 <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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328 <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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329 <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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330 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details">
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331 <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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332 <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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333 </param>
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334 <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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335 <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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336 </when>
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337 <when value="no">
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338 <!-- do nothing -->
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339 </when>
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340 </conditional>
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341 <conditional name="alignment_options">
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342 <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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343 <option value="yes">Yes</option>
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344 <option value="no" selected="true">No</option>
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345 </param>
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346 <when value="yes">
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347 <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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348 <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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349 <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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350 <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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351 <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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352 <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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353 <param name="ignore_quals" type="boolean" truevalue="--ignore-quals" falsevalue="" selected="False" 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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354 <param name="nofw" type="boolean" truevalue="--nofw" falsevalue="" selected="False" 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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355 <param name="norc" type="boolean" truevalue="--norc" falsevalue="" selected="False" 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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356 <param name="no_1mm_upfront" type="boolean" truevalue="--no-1mm-upfront" falsevalue="" selected="False" 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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357 <conditional name="align_mode">
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358 <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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359 <option value="end-to-end" selected="True">End to End (--end-to-end)</option>
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360 <option value="local">Local (--local)</option>
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361 </param>
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362 <when value="end-to-end">
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363 <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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364 </when>
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365 <when value="local">
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366 <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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367 </when>
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368 </conditional>
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369 </when>
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370 <when value="no">
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371 <!-- do nothing -->
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372 </when>
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373 </conditional>
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374 <conditional name="scoring_options">
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375 <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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376 <option value="yes">Yes</option>
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377 <option value="no" selected="true">No</option>
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378 </param>
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379 <when value="yes">
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380 <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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381 <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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382 <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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383 <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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384 <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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385 <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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386 <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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387 </when>
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388 <when value="no">
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389 <!-- do nothing -->
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390 </when>
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391 </conditional>
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392 <conditional name="reporting_options">
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393 <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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394 <option value="no" selected="true">No, do not set</option>
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395 <option value="k">Set -k option and enter -k value</option>
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396 <option value="a">Set -a option</option>
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397 </param>
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398 <when value="no">
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399 <!-- do nothing -->
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400 </when>
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401 <when value="k">
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402 <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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403 </when>
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404 <when value="a">
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405 <!-- do nothing here; set -a flag on the command line-->
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406 </when>
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407 </conditional>
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408 <conditional name="effort_options">
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409 <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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410 <option value="yes">Yes</option>
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411 <option value="no" selected="true">No</option>
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412 </param>
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413 <when value="yes">
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414 <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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415 <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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416 </when>
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417 <when value="no">
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418 <!-- do nothing -->
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419 </when>
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420 </conditional>
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421
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422 <conditional name="sam_options">
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423 <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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424 <option value="yes">Yes</option>
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425 <option value="no" selected="true">No</option>
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426 </param>
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427 <when value="yes">
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428 <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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429 <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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430 </when>
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431 <when value="no">
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432 <!-- do nothing -->
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433 </when>
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434 </conditional>
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435 <conditional name="other_options">
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436 <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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437 <option value="yes">Yes</option>
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438 <option value="no" selected="true">No</option>
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439 </param>
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440 <when value="yes">
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441 <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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442 <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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443 <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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444 </when>
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445 <when value="no">
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446 <!-- do nothing -->
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447 </when>
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448 </conditional>
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449 <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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450 </when>
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451 </conditional>
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452 <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie2 mapping statistics to the history" />
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453 </inputs>
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454
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455 <!-- define outputs -->
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456
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457 <outputs>
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458
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459 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" >
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460 <filter>library['unaligned_file'] is True</filter>
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461 <actions>
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462 <conditional name="library.type">
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463 <when value="single">
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464 <action type="format">
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465 <option type="from_param" name="library.input_1" param_attribute="ext" />
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466 </action>
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467 </when>
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468 <when value="paired">
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469 <action type="format">
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470 <option type="from_param" name="library.input_1" param_attribute="ext" />
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471 </action>
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472 </when>
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473 <when value="paired_collection">
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474 <action type="format">
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475 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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476 </action>
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477 </when>
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478 </conditional>
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479 </actions>
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480 </data>
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481 <data format="fastqsanger" name="output_aligned_reads_l" label="${tool.name} on ${on_string}: aligned reads (L)" >
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482 <filter>library['aligned_file'] is True</filter>
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483 <actions>
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484 <conditional name="library.type">
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485 <when value="single">
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486 <action type="format">
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487 <option type="from_param" name="library.input_1" param_attribute="ext" />
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488 </action>
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489 </when>
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490 <when value="paired">
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491 <action type="format">
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492 <option type="from_param" name="library.input_1" param_attribute="ext" />
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493 </action>
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494 </when>
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495 <when value="paired_collection">
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496 <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
497 <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
498 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
499 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
500 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
501 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
502 </data>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
503 <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
504 <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
505 <actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
506 <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
507 <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
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_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
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 <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
513 <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
514 <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
515 </action>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
516 </when>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
517 </conditional>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
518 </actions>
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
devteam
parents: 8
diff changeset
519 </data>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
520 <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
521 <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
522 <actions>
7
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
523 <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
524 <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
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_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
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 <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
530 <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
531 <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
532 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
533 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
534 </conditional>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
535 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
536 </data>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
537
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
538 <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
539 <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
540 <actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
541 <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
542 <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
543 <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
544 <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
545 <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
546 <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
547 </option>
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 <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
551 <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
552 <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
553 </action>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
554 </when>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
555 </conditional>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
556 </actions>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
557 </data>
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
558
4f92dccc808a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 6
diff changeset
559 <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
560 <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
561 <actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
562 <conditional name="reference_genome.source">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
563 <when value="indexed">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
564 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
565 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
566 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
567 <filter type="param_value" ref="reference_genome.index" column="0"/>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
568 </option>
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 <when value="history">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
572 <action type="metadata" name="dbkey">
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
573 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" />
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
574 </action>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
575 </when>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
576 </conditional>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
577 </actions>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
578 </data>
10
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
579 <data format="txt" name="mapping_stats" label="${tool.name} on ${on_string}: mapping stats">
a9d4f71dbfb0 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit 320f7fb84d2fda19f6cccdb38b4ef49edec4169d
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parents: 8
diff changeset
580 <filter>save_mapping_stats is True</filter>
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parents: 8
diff changeset
581 </data>
3
ceb6467e276c Uploaded
devteam
parents: 2
diff changeset
582
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
583 </outputs>
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
584
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
585 <tests>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
586 <test>
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
587 <!-- basic test on single paired default run -->
2
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
588 <param name="type" value="paired"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
589 <param name="selection" value="no"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
590 <param name="paired_options_selector" value="no"/>
0
96d2e31a3938 Imported from capsule None
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parents:
diff changeset
591 <param name="unaligned_file" value="false"/>
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
592 <param name="analysis_type_selector" value="simple"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
593 <param name="source" value="history" />
2
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
594 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
595 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
c1ec08cb34f9 Uploaded
devteam
parents: 0
diff changeset
596 <param name="own_file" value="bowtie2-ref.fasta" />
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devteam
parents: 0
diff changeset
597 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
0
96d2e31a3938 Imported from capsule None
devteam
parents:
diff changeset
598 </test>
5
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devteam
parents: 4
diff changeset
599 <test>
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devteam
parents: 4
diff changeset
600 <!-- basic test on single paired default run -->
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
601 <param name="type" value="paired"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
602 <param name="selection" value="no"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
603 <param name="paired_options_selector" value="no"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
604 <param name="unaligned_file" value="false"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
605 <param name="analysis_type_selector" value="simple"/>
42bb952b4e3c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents: 4
diff changeset
606 <param name="rg_selector" value="set"/>
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607 <param name="ID" value="rg1"/>
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608 <param name="PL" value="CAPILLARY"/>
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609 <param name="source" value="history" />
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610 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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611 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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612 <param name="own_file" value="bowtie2-ref.fasta" />
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613 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
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614 </test>
10
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615 <test>
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616 <!-- basic test on single paired default run with stats-->
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617 <param name="type" value="paired"/>
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618 <param name="selection" value="no"/>
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619 <param name="paired_options_selector" value="no"/>
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620 <param name="unaligned_file" value="false"/>
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621 <param name="analysis_type_selector" value="simple"/>
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622 <param name="source" value="history" />
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623 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
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624 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
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625 <param name="own_file" value="bowtie2-ref.fasta" />
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626 <param name="save_mapping_stats" value="true" />
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627 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
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628 <output name="mapping_stats" file="bowtie2-stats.out" ftype="txt"/>
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629 </test>
0
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630 </tests>
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631
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632 <help>
2
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633
0
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634 **Bowtie2 Overview**
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635
2
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636 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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637 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead.
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638
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639 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/
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640 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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641 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf
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642
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643 -----
0
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644
2
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645 **Selecting reference genomes for Bowtie2**
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646
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647 Galaxy wrapper for Bowtie2 allows you select between precomputed and user-defined indices for reference genomes using **Will you select a reference genome from your history or use a built-in index?** flag. This flag has two options:
0
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648
2
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649 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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650 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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651
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652 If your genome of interest is not listed here you have two choices:
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653
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654 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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655 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history and build index** option.
0
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656
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657 ------
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658
2
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659 .. class:: infomark
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660
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661 **Bowtie2 options**
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662
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663 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below.
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664
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665 -----
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666
0
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667 **Inputs**
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668
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669 Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files.
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670
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671 ------
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672
2
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673 **Input options**::
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674
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675 -s/--skip &lt;int&gt;
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676 Skip (i.e. do not align) the first `&lt;int&gt;` reads or pairs in the input.
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677
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678 -u/--qupto &lt;int&gt;
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679 Align the first `&lt;int&gt;` reads or read pairs from the input (after the
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680 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit.
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681
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682 -5/--trim5 &lt;int&gt;
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683 Trim `&lt;int&gt;` bases from 5' (left) end of each read before alignment (default: 0).
0
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684
2
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685 -3/--trim3 &lt;int&gt;
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686 Trim `&lt;int&gt;` bases from 3' (right) end of each read before alignment (default: 0).
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687
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688 --phred33
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689 Input qualities are ASCII chars equal to the Phred quality plus 33. This is
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690 also called the "Phred+33" encoding, which is used by the very latest Illumina
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691 pipelines.
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692
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693 --phred64
3
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694 Input qualities are ASCII chars equal to the Phred quality plus 64. This is
2
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695 also called the "Phred+64" encoding.
0
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696
2
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697 --solexa-quals
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698 Convert input qualities from Solexa Phred quality (which can be negative) to
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699 Phred Phred quality (which can't). This scheme was used in older Illumina GA
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700 Pipeline versions (prior to 1.3). Default: off.
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701
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702 --int-quals
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703 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`....
3
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704 Integers are treated as being on the Phred quality scale unless
2
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705 `--solexa-quals` is also specified. Default: off.
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706
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707 ------
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708
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709 **Presets in `--end-to-end` mode**::
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710
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711 --very-fast
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712 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50`
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713
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714 --fast
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715 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50`
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716
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717 --sensitive
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718 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode)
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719
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720 --very-sensitive
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721 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
0
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722
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723 ------
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724
2
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725 **Presets options in `--local` mode**::
0
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726
2
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727 --very-fast-local
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728 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00`
0
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729
2
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730 --fast-local
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731 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75`
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732
2
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733 --sensitive-local
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734 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode)
0
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735
2
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736 --very-sensitive-local
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737 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50`
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738
0
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739 ------
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740
2
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741 **Alignment options**::
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742
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743 -N &lt;int&gt;
3
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744 Sets the number of mismatches to allowed in a seed alignment during multiseed
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745 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower
2
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746 (often much slower) but increases sensitivity. Default: 0.
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747
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748 -L &lt;int&gt;
3
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749 Sets the length of the seed substrings to align during multiseed alignment.
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750 Smaller values make alignment slower but more sensitive. Default: the
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751 `--sensitive` preset is used by default, which sets `-L` to 22 in
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752 `--end-to-end` mode and to 20 in `--local` mode.
2
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753
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754 -i &lt;func&gt;
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755 Sets a function governing the interval between seed substrings to use during
3
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756 multiseed alignment. For instance, if the read has 30 characers, and seed
2
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757 length is 10, and the seed interval is 6, the seeds extracted will be:
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758
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759 Read: TAGCTACGCTCTACGCTATCATGCATAAAC
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760 Seed 1 fw: TAGCTACGCT
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761 Seed 1 rc: AGCGTAGCTA
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762 Seed 2 fw: CGCTCTACGC
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763 Seed 2 rc: GCGTAGAGCG
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764 Seed 3 fw: ACGCTATCAT
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765 Seed 3 rc: ATGATAGCGT
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diff changeset
766 Seed 4 fw: TCATGCATAA
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parents: 0
diff changeset
767 Seed 4 rc: TTATGCATGA
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parents: 0
diff changeset
768
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parents: 0
diff changeset
769 Since it's best to use longer intervals for longer reads, this parameter sets
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parents: 0
diff changeset
770 the interval as a function of the read length, rather than a single
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parents: 0
diff changeset
771 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the
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parents: 0
diff changeset
772 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
773 If the function returns a result less than
2
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parents: 0
diff changeset
774 1, it is rounded up to 1. Default: the `--sensitive` preset is used by
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parents: 0
diff changeset
775 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
776 in `--local` mode.
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parents: 0
diff changeset
777
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parents: 0
diff changeset
778 --n-ceil &lt;func&gt;
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parents: 0
diff changeset
779 Sets a function governing the maximum number of ambiguous characters (usually
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parents: 0
diff changeset
780 `N`s and/or `.`s) allowed in a read as a function of read length. For instance,
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devteam
parents: 0
diff changeset
781 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`,
3
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devteam
parents: 2
diff changeset
782 where x is the read length. Reads exceeding this ceiling are filtered out.
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parents: 2
diff changeset
783 Default: `L,0,0.15`.
2
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parents: 0
diff changeset
784
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parents: 0
diff changeset
785 --dpad &lt;int&gt;
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parents: 0
diff changeset
786 "Pads" dynamic programming problems by `&lt;int&gt;` columns on either side to allow
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parents: 0
diff changeset
787 gaps. Default: 15.
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parents: 0
diff changeset
788
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parents: 0
diff changeset
789 --gbar &lt;int&gt;
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parents: 0
diff changeset
790 Disallow gaps within `&lt;int&gt;` positions of the beginning or end of the read.
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parents: 0
diff changeset
791 Default: 4.
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parents: 0
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792
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parents: 0
diff changeset
793 --ignore-quals
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parents: 0
diff changeset
794 When calculating a mismatch penalty, always consider the quality value at the
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parents: 0
diff changeset
795 mismatched position to be the highest possible, regardless of the actual value.
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parents: 0
diff changeset
796 I.e. input is treated as though all quality values are high. This is also the
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parents: 0
diff changeset
797 default behavior when the input doesn't specify quality values (e.g. in `-f`,
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parents: 0
diff changeset
798 `-r`, or `-c` modes).
0
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799
2
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diff changeset
800 --nofw/--norc
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parents: 0
diff changeset
801 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to
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parents: 0
diff changeset
802 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will
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parents: 0
diff changeset
803 not attempt to align unpaired reads against the reverse-complement (Crick)
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parents: 0
diff changeset
804 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the
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parents: 0
diff changeset
805 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those
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parents: 0
diff changeset
806 paired-end configurations corresponding to fragments from the reverse-complement
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parents: 0
diff changeset
807 (Crick) strand. Default: both strands enabled.
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parents: 0
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808
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parents: 0
diff changeset
809 --no-1mm-upfront
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parents: 0
diff changeset
810 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch
3
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parents: 2
diff changeset
811 end-to-end alignment for the read *before* trying the multiseed heuristic. Such
2
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parents: 0
diff changeset
812 alignments can be found very quickly, and many short read alignments have exact or
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parents: 0
diff changeset
813 near-exact end-to-end alignments. However, this can lead to unexpected
3
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parents: 2
diff changeset
814 alignments when the user also sets options governing the multiseed heuristic,
2
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diff changeset
815 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal
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parents: 0
diff changeset
816 to the length of the read, the user will be surprised to find 1-mismatch alignments
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parents: 0
diff changeset
817 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end
3
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parents: 2
diff changeset
818 alignments before using the multiseed heuristic, which leads to the expected
2
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parents: 0
diff changeset
819 behavior when combined with options such as `-L` and `-N`. This comes at the
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parents: 0
diff changeset
820 expense of speed.
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parents: 0
diff changeset
821
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parents: 0
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822 --end-to-end
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parents: 0
diff changeset
823 In this mode, Bowtie 2 requires that the entire read align from one end to the
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parents: 0
diff changeset
824 other, without any trimming (or "soft clipping") of characters from either end.
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parents: 0
diff changeset
825 The match bonus `--ma` always equals 0 in this mode, so all alignment scores
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parents: 0
diff changeset
826 are less than or equal to 0, and the greatest possible alignment score is 0.
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parents: 0
diff changeset
827 This is mutually exclusive with `--local`. `--end-to-end` is the default mode.
0
96d2e31a3938 Imported from capsule None
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828
2
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parents: 0
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829 --local
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parents: 0
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830 In this mode, Bowtie 2 does not require that the entire read align from one end
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parents: 0
diff changeset
831 to the other. Rather, some characters may be omitted ("soft clipped") from the
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parents: 0
diff changeset
832 ends in order to achieve the greatest possible alignment score. The match bonus
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parents: 0
diff changeset
833 `--ma` is used in this mode, and the best possible alignment score is equal to
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parents: 0
diff changeset
834 the match bonus (`--ma`) times the length of the read. Specifying `--local`
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parents: 0
diff changeset
835 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying
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parents: 0
diff changeset
836 the local version of the preset (`--very-fast-local`). This is mutually
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parents: 0
diff changeset
837 exclusive with `--end-to-end`. `--end-to-end` is the default mode.
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parents: 0
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838
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parents: 0
diff changeset
839 -----
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parents: 0
diff changeset
840
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parents: 0
diff changeset
841 **Scoring options**::
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parents: 0
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842
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parents: 0
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843 --ma &lt;int&gt;
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parents: 0
diff changeset
844 Sets the match bonus. In `--local` mode `&lt;int&gt;` is added to the alignment
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parents: 0
diff changeset
845 score for each position where a read character aligns to a reference character
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parents: 0
diff changeset
846 and the characters match. Not used in `--end-to-end` mode. Default: 2.
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parents: 0
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847
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parents: 0
diff changeset
848 --mp MX,MN
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parents: 0
diff changeset
849 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A
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parents: 0
diff changeset
850 number less than or equal to `MX` and greater than or equal to `MN` is
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parents: 0
diff changeset
851 subtracted from the alignment score for each position where a read character
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parents: 0
diff changeset
852 aligns to a reference character, the characters do not match, and neither is an
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parents: 0
diff changeset
853 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`.
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diff changeset
854 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )`
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parents: 0
diff changeset
855 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2.
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parents: 0
diff changeset
856
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parents: 0
diff changeset
857 --np &lt;int&gt;
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parents: 0
diff changeset
858 Sets penalty for positions where the read, reference, or both, contain an
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parents: 0
diff changeset
859 ambiguous character such as `N`. Default: 1.
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parents: 0
diff changeset
860
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parents: 0
diff changeset
861 --rdg &lt;int1&gt;,&lt;int2&gt;
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parents: 0
diff changeset
862 Sets the read gap open (`&lt;int1&gt;`) and extend (`&lt;int2&gt;`) penalties. A read gap of
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parents: 0
diff changeset
863 length N gets a penalty of `&lt;int1&gt;` + N * `&lt;int2&gt;`. Default: 5, 3.
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parents: 0
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864
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diff changeset
865 --rfg &lt;int1&gt;,&lt;int2&gt;
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parents: 0
diff changeset
866 Sets the reference gap open (`&lt;int1&gt;`) and extend (`&lt;int2&gt;`) penalties. A
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parents: 0
diff changeset
867 reference gap of length N gets a penalty of `&lt;int1&gt;` + N * `&lt;int2&gt;`. Default:
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parents: 0
diff changeset
868 5, 3.
0
96d2e31a3938 Imported from capsule None
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parents:
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869
2
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parents: 0
diff changeset
870 --score-min &lt;func&gt;
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parents: 0
diff changeset
871 Sets a function governing the minimum alignment score needed for an alignment to
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parents: 0
diff changeset
872 be considered "valid" (i.e. good enough to report). This is a function of read
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parents: 0
diff changeset
873 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f`
3
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parents: 2
diff changeset
874 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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parents: 0
diff changeset
875 the default in `--local` mode is `G,20,8`.
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parents: 0
diff changeset
876
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parents: 0
diff changeset
877 -----
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parents: 0
diff changeset
878
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parents: 0
diff changeset
879 **Reporting options**::
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parents: 0
diff changeset
880
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parents: 0
diff changeset
881 -k &lt;int&gt;
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parents: 0
diff changeset
882 By default, `bowtie2` searches for distinct, valid alignments for each read.
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parents: 0
diff changeset
883 When it finds a valid alignment, it continues looking for alignments that are
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parents: 0
diff changeset
884 nearly as good or better. The best alignment found is reported (randomly
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parents: 0
diff changeset
885 selected from among best if tied). Information about the best alignments is
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parents: 0
diff changeset
886 used to estimate mapping quality and to set SAM optional fields, such as
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parents: 0
diff changeset
887 `AS:i` and `XS:i`.
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
888
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parents: 0
diff changeset
889 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
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parents: 0
diff changeset
890 searches for at most `&lt;int&gt;` distinct, valid alignments for each read. The
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devteam
parents: 0
diff changeset
891 search terminates when it can't find more distinct valid alignments, or when it
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parents: 0
diff changeset
892 finds `&lt;int&gt;`, whichever happens first. All alignments found are reported in
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parents: 0
diff changeset
893 descending order by alignment score. The alignment score for a paired-end
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parents: 0
diff changeset
894 alignment equals the sum of the alignment scores of the individual mates. Each
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parents: 0
diff changeset
895 reported read or pair alignment beyond the first has the SAM 'secondary' bit
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parents: 0
diff changeset
896 (which equals 256) set in its FLAGS field. For reads that have more than
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parents: 0
diff changeset
897 `&lt;int&gt;` distinct, valid alignments, `bowtie2` does not guarantee that the
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parents: 0
diff changeset
898 `&lt;int&gt;` alignments reported are the best possible in terms of alignment score.
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parents: 0
diff changeset
899 `-k` is mutually exclusive with `-a`.
0
96d2e31a3938 Imported from capsule None
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parents:
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900
2
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parents: 0
diff changeset
901 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when
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parents: 0
diff changeset
902 aligning reads to long, repetitive genomes large `-k` can be very, very slow.
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parents: 0
diff changeset
903
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parents: 0
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904 -a
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parents: 0
diff changeset
905 Like `-k` but with no upper limit on number of alignments to search for. `-a`
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parents: 0
diff changeset
906 is mutually exclusive with `-k`.
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parents: 0
diff changeset
907
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parents: 0
diff changeset
908 Note: Bowtie 2 is not designed with `-a` mode in mind, and when
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parents: 0
diff changeset
909 aligning reads to long, repetitive genomes this mode can be very, very slow.
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parents: 0
diff changeset
910
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parents: 0
diff changeset
911 -----
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parents: 0
diff changeset
912
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parents: 0
diff changeset
913 **Effort options**::
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parents: 0
diff changeset
914
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parents: 0
diff changeset
915 -D &lt;int&gt;
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parents: 0
diff changeset
916 Up to `&lt;int&gt;` consecutive seed extension attempts can "fail" before Bowtie 2
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parents: 0
diff changeset
917 moves on, using the alignments found so far. A seed extension "fails" if it
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parents: 0
diff changeset
918 does not yield a new best or a new second-best alignment. This limit is
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parents: 0
diff changeset
919 automatically adjusted up when -k or -a are specified. Default: 15.
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parents: 0
diff changeset
920
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parents: 0
diff changeset
921 -R &lt;int&gt;
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parents: 0
diff changeset
922 `&lt;int&gt;` is the maximum number of times Bowtie 2 will "re-seed" reads with
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parents: 0
diff changeset
923 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads
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parents: 0
diff changeset
924 (same length, same number of mismatches allowed) at different offsets and
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parents: 0
diff changeset
925 searches for more alignments. A read is considered to have repetitive seeds if
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parents: 0
diff changeset
926 the total number of seed hits divided by the number of seeds that aligned at
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parents: 0
diff changeset
927 least once is greater than 300. Default: 2.
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parents: 0
diff changeset
928
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parents: 0
diff changeset
929 -----
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parents: 0
diff changeset
930
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parents: 0
diff changeset
931 **Paired-end options**::
0
96d2e31a3938 Imported from capsule None
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parents:
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932
2
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parents: 0
diff changeset
933 -I/--minins &lt;int&gt;
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parents: 0
diff changeset
934 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is
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parents: 0
diff changeset
935 specified and a paired-end alignment consists of two 20-bp alignments in the
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parents: 0
diff changeset
936 appropriate orientation with a 20-bp gap between them, that alignment is
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parents: 0
diff changeset
937 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not
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parents: 0
diff changeset
938 be valid in that case. If trimming options `-3` or `-5` are also used, the
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parents: 0
diff changeset
939 `-I` constraint is applied with respect to the untrimmed mates.
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parents: 0
diff changeset
940
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parents: 0
diff changeset
941 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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parents: 0
diff changeset
942 run. This is because larger differences bewteen `-I` and `-X` require that
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parents: 0
diff changeset
943 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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parents: 0
diff changeset
944 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
c1ec08cb34f9 Uploaded
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parents: 0
diff changeset
945 efficient.
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parents: 0
diff changeset
946
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parents: 0
diff changeset
947 Default: 0 (essentially imposing no minimum)
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parents: 0
diff changeset
948
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parents: 0
diff changeset
949 -X/--maxins &lt;int&gt;
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parents: 0
diff changeset
950 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100`
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parents: 0
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951 is specified and a paired-end alignment consists of two 20-bp alignments in the
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952 proper orientation with a 60-bp gap between them, that alignment is considered
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953 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in
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954 that case. If trimming options `-3` or `-5` are also used, the `-X`
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955 constraint is applied with respect to the untrimmed mates, not the trimmed
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956 mates.
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957
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958 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will
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959 run. This is because larger differences bewteen `-I` and `-X` require that
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960 Bowtie 2 scan a larger window to determine if a concordant alignment exists.
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961 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very
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962 efficient.
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963
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964 Default: 500.
0
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965
2
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966 --fr/--rf/--ff
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967 The upstream/downstream mate orientations for a valid paired-end alignment
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968 against the forward reference strand. E.g., if `--fr` is specified and there is
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969 a candidate paired-end alignment where mate 1 appears upstream of the reverse
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970 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are
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971 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse
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972 complement of mate 1 and all other constraints are met, that too is valid.
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973 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a
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974 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1
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975 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate
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976 for Illumina's Paired-end Sequencing Assay).
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977
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978 --no-mixed
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979 By default, when `bowtie2` cannot find a concordant or discordant alignment for
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980 a pair, it then tries to find alignments for the individual mates. This option
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981 disables that behavior.
0
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982
2
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983 --no-discordant
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984 By default, `bowtie2` looks for discordant alignments if it cannot find any
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985 concordant alignments. A discordant alignment is an alignment where both mates
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986 align uniquely, but that does not satisfy the paired-end constraints
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987 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior.
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988
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989 --dovetail
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990 If the mates "dovetail", that is if one mate alignment extends past the
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diff changeset
991 beginning of the other such that the wrong mate begins upstream, consider that
3
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992 to be concordant. Default: mates cannot dovetail in a concordant alignment.
2
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993
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994 --no-contain
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995 If one mate alignment contains the other, consider that to be non-concordant.
3
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996 Default: a mate can contain the other in a concordant alignment.
2
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997
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998 --no-overlap
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999 If one mate alignment overlaps the other at all, consider that to be
3
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1000 non-concordant. Default: mates can overlap in a concordant alignment.
2
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1001
0
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1002 ------
96d2e31a3938 Imported from capsule None
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1003
2
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diff changeset
1004 **SAM options**::
0
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1005
2
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1006 --rg-id &lt;text&gt;
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1007 Set the read group ID to `&lt;text&gt;`. This causes the SAM `@RG` header line to be
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1008 printed, with `&lt;text&gt;` as the value associated with the `ID:` tag. It also
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1009 causes the `RG:Z:` extra field to be attached to each SAM output record, with
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1010 value set to `&lt;text&gt;`.
0
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1011
2
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1012 --rg &lt;text&gt;
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1013 Add `&lt;text&gt;` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the
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1014 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id`
3
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1015 must also be specified. This is because the `ID` tag is required by the SAM
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1016 Specification. Specify `--rg` multiple times to set multiple fields. See the
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1017 SAM Specification for details about what fields are legal.
0
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1018
2
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1019 --omit-sec-seq
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1020 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ`
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1021 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix
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1022 in those fields instead.
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1023
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1024 -----
0
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1025
2
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1026 **Other options**::
0
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1027
2
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1028 --reorder
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1029 Guarantees that output SAM records are printed in an order corresponding to the
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1030 order of the reads in the original input file, even when `-p` is set greater
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1031 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie
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1032 2 to run somewhat slower and use somewhat more memory then if `--reorder` were
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1033 not specified. Has no effect if `-p` is set to 1, since output order will
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1034 naturally correspond to input order in that case.
0
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1035
2
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1036 --seed &lt;int&gt;
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1037 Use `&lt;int&gt;` as the seed for pseudo-random number generator. Default: 0.
0
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1038
2
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1039 --non-deterministic
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1040 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It
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1041 seeds the generator with a number derived from (a) the read name, (b) the
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1042 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed`
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1043 option. This means that if two reads are identical (same name, same
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1044 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s)
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1045 for both, even if there was ambiguity. When `--non-deterministic` is specified,
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1046 Bowtie 2 re-initializes its pseudo-random generator for each read using the
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1047 current time. This means that Bowtie 2 will not necessarily report the same
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1048 alignment for two identical reads. This is counter-intuitive for some users,
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1049 but might be more appropriate in situations where the input consists of many
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1050 identical reads.
0
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1051
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1052 </help>
2
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1053 <citations>
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1054 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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1055 <citation type="doi">10.1038/nmeth.1923</citation>
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1056 </citations>
0
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1057 </tool>