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annotate bowtie2_wrapper.xml @ 5:5cfa4b6db588 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:13:27 -0400 |
| parents | 2a6cfe8997aa |
| children | 76231961d33b |
| rev | line source |
|---|---|
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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1 <tool id="bowtie2" name="Bowtie2" version="0.6"> |
| 2 | 2 <!-- Wrapper compatible with Bowtie version 2.2.4 --> |
| 3 <description>- map reads against reference genome</description> | |
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4 <macros> |
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5 <import>read_group_macros.xml</import> |
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6 </macros> |
| 0 | 7 <version_command>bowtie2 --version</version_command> |
| 8 <requirements> | |
| 2 | 9 <requirement type="package" version="2.2.4">bowtie2</requirement> |
| 0 | 10 <requirement type="package" version="0.1.18">samtools</requirement> |
| 11 </requirements> | |
| 12 <command> | |
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13 |
| 0 | 14 ## prepare bowtie2 index |
| 15 #set index_path = '' | |
| 16 #if str($reference_genome.source) == "history": | |
| 2 | 17 bowtie2-build "$reference_genome.own_file" genome && |
| 18 ln -s "$reference_genome.own_file" genome.fa && | |
| 0 | 19 #set index_path = 'genome' |
| 20 #else: | |
| 21 #set index_path = $reference_genome.index.fields.path | |
| 22 #end if | |
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23 |
| 0 | 24 ## execute bowtie2 |
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25 |
| 0 | 26 bowtie2 |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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27 |
| 0 | 28 ## number of threads |
| 29 -p \${GALAXY_SLOTS:-4} | |
| 30 | |
| 31 ## index file path | |
| 32 -x $index_path | |
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33 |
| 2 | 34 ## Fastq inputs |
| 35 #if str( $library.type ) == "single": | |
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36 -U "${library.input_1}" |
| 2 | 37 #if str( $library.unaligned_file ) == "true": |
| 0 | 38 --un $output_unaligned_reads_l |
| 39 #end if | |
| 2 | 40 #elif str( $library.type ) == "paired": |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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41 -1 "${library.input_1}" |
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42 -2 "${library.input_2}" |
| 2 | 43 #if str( $library.paired_options.paired_options_selector ) == "yes": |
| 44 -I "${library.paired_options.I}" | |
| 45 -X "${library.paired_options.X}" | |
| 46 ${library.paired_options.fr_rf_ff} | |
| 47 ${library.paired_options.no_mixed} | |
| 48 ${library.paired_options.no_discordant} | |
| 49 ${library.paired_options.dovetail} | |
| 50 ${library.paired_options.no_contain} | |
| 51 ${library.paired_options.no_overlap} | |
| 52 #end if | |
| 53 #if str( $library.unaligned_file ) == "true": | |
| 54 --un-conc $output_unaligned_reads_l | |
| 55 #end if | |
| 0 | 56 #else |
| 2 | 57 ## prepare collection |
| 58 -1 $library.input_1.forward | |
| 59 -2 $library.input_1.reverse | |
| 60 #if str( $library.paired_options.paired_options_selector ) == "yes": | |
| 61 -I "${library.paired_options.I}" | |
| 62 -X "${library.paired_options.X}" | |
| 63 ${library.paired_options.fr_rf_ff} | |
| 64 ${library.paired_options.no_mixed} | |
| 65 ${library.paired_options.no_discordant} | |
| 66 ${library.paired_options.dovetail} | |
| 67 ${library.paired_options.no_contain} | |
| 68 ${library.paired_options.no_overlap} | |
| 69 #end if | |
| 70 #if str( $library.unaligned_file ) == "true": | |
| 0 | 71 --un-conc $output_unaligned_reads_l |
| 72 #end if | |
| 73 #end if | |
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74 |
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75 ## Read group information. |
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76 @define_read_group_helpers@ |
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77 #if str( $library.type ) == "single": |
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78 #set $rg_auto_name = $read_group_name_default($library.input_1) |
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79 #elif str( $library.type ) == "paired": |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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80 #set $rg_auto_name = $read_group_name_default($library.input_1, $library.input_2) |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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81 #else |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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82 #set $rg_auto_name = $read_group_name_default($library.input_1) |
| 2 | 83 #end if |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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84 @set_use_rg_var@ |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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85 @set_read_group_vars@ |
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86 #if $use_rg |
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87 $format_read_group("", $rg_id, '"', arg='--rg-id ') |
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88 $format_read_group("SM:", $rg_sm, '"', arg='--rg ') |
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89 $format_read_group("PL:", $rg_pl, '"', arg='--rg ') |
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90 $format_read_group("LB:", $rg_lb, '"', arg='--rg ') |
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91 $format_read_group("CN:", $rg_cn, '"', arg='--rg ') |
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92 $format_read_group("DS:", $rg_ds, '"', arg='--rg ') |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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93 $format_read_group("DT:", $rg_dt, '"', arg='--rg ') |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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94 $format_read_group("FO:", $rg_fo, '"', arg='--rg ') |
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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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95 $format_read_group("KS:", $rg_ks, '"', arg='--rg ') |
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96 $format_read_group("PG:", $rg_pg, '"', arg='--rg ') |
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97 $format_read_group("PI:", $rg_pi, '"', arg='--rg ') |
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98 $format_read_group("PU:", $rg_pu, '"', arg='--rg ') |
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99 #end if |
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100 |
| 2 | 101 ## Analysis type |
| 102 #if ( str( $analysis_type.analysis_type_selector ) == "simple" and str( $analysis_type.presets ) != "no_presets" ): | |
| 103 $analysis_type.presets | |
| 104 #elif str( $analysis_type.analysis_type_selector ) == "full": | |
| 105 #if str( $analysis_type.input_options.input_options_selector ) == "yes": | |
| 106 --skip "${analysis_type.input_options.skip}" | |
| 107 --qupto "${analysis_type.input_options.qupto}" | |
| 108 --trim5 "${analysis_type.input_options.trim5}" | |
| 109 --trim3 "${analysis_type.input_options.trim3}" | |
| 110 ${analysis_type.input_options.qv_encoding} | |
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111 ${analysis_type.input_options.solexa_quals} |
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112 ${analysis_type.input_options.int_quals} |
| 0 | 113 #end if |
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114 |
| 2 | 115 #if str( $analysis_type.alignment_options.alignment_options_selector ) == "yes": |
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116 -N "${analysis_type.alignment_options.N}" |
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117 -L "${analysis_type.alignment_options.L}" |
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118 -i "${analysis_type.alignment_options.i}" |
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119 --n-ceil "${analysis_type.alignment_options.n_ceil}" |
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120 --dpad "${analysis_type.alignment_options.dpad}" |
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121 --gbar "${analysis_type.alignment_options.gbar}" |
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122 ${analysis_type.alignment_options.ignore_quals} |
| 2 | 123 ${analysis_type.alignment_options.nofw} |
| 124 ${analysis_type.alignment_options.norc} | |
| 125 ${analysis_type.alignment_options.no_1mm_upfront} | |
| 126 #if str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "end-to-end": | |
| 127 --end-to-end | |
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128 --score-min "${analysis_type.alignment_options.align_mode.score_min_ete}" |
| 2 | 129 #elif str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local": |
| 130 --local | |
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131 --score-min "${analysis_type.alignment_options.align_mode.score_min_loc}" |
| 2 | 132 #end if |
| 133 #end if | |
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134 |
| 2 | 135 #if str( $analysis_type.scoring_options.scoring_options_selector ) == "yes": |
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136 #if ( str( $analysis_type.alignment_options.alignment_options_selector ) == "yes" and str( $analysis_type.alignment_options.align_mode.align_mode_selector ) == "local" ): |
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137 --ma "${analysis_type.scoring_options.ma}" |
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138 #end if |
| 2 | 139 --mp "${analysis_type.scoring_options.mp}" |
| 140 --np "${analysis_type.scoring_options.np}" | |
| 141 --rdg "${analysis_type.scoring_options.rdg_read_open},${analysis_type.scoring_options.rdg_read_extend}" | |
| 142 --rfg "${analysis_type.scoring_options.rfg_ref_open},${analysis_type.scoring_options.rfg_ref_extend}" | |
| 143 #end if | |
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144 |
| 2 | 145 #if str( $analysis_type.reporting_options.reporting_options_selector ) == "k": |
| 146 -k "${analysis_type.reporting_options.k}" | |
| 147 #elif str( $analysis_type.reporting_options.reporting_options_selector ) == "a": | |
| 148 -a | |
| 149 #end if | |
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150 |
| 2 | 151 #if str( $analysis_type.effort_options.effort_options_selector ) == "yes": |
| 152 -D "${analysis_type.effort_options.D}" | |
| 153 -R "${analysis_type.effort_options.R}" | |
| 154 #end if | |
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155 |
| 2 | 156 #if str( $analysis_type.sam_options.sam_options_selector ) == "yes": |
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157 ${analysis_type.sam_options.no_unal} |
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158 ${analysis_type.sam_options.omit_sec_seq} |
| 2 | 159 #end if |
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160 |
| 2 | 161 #if str( $analysis_type.other_options.other_options_selector ) == "yes": |
| 162 ${analysis_type.other_options.reorder} | |
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163 ${analysis_type.other_options.non_deterministic} |
| 2 | 164 --seed "${analysis_type.other_options.seed}" |
| 0 | 165 #end if |
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166 |
| 2 | 167 #elif str( $analysis_type.analysis_type_selector ) == "cline": |
| 168 ${analysis_type.cline} | |
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169 #end if |
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170 |
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171 ## output file |
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172 #if ( str( $analysis_type.analysis_type_selector ) != "full" or str( $analysis_type.sam_opt ) != "true" ): |
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173 | samtools view -Su - | samtools sort -o - - > $output |
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174 #else |
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175 > $output_sam |
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176 #end if |
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177 |
| 0 | 178 ## rename unaligned sequence files |
| 179 #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r: | |
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180 #from os.path import splitext |
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181 #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) ) |
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182 && mv "${ _unaligned_root }.1${_unaligned_ext}" "${ output_unaligned_reads_l }" |
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183 && mv "${ _unaligned_root }.2${_unaligned_ext}" "${ output_unaligned_reads_r }" |
| 0 | 184 #end if |
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185 |
| 0 | 186 </command> |
| 187 <!-- basic error handling --> | |
| 188 <stdio> | |
| 189 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 190 </stdio> | |
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191 |
| 0 | 192 <inputs> |
| 193 <!-- single/paired --> | |
| 194 <conditional name="library"> | |
| 2 | 195 <param name="type" type="select" label="Is this single or paired library"> |
| 0 | 196 <option value="single">Single-end</option> |
| 197 <option value="paired">Paired-end</option> | |
| 2 | 198 <option value="paired_collection">Paired-end Dataset Collection</option> |
| 0 | 199 </param> |
| 2 | 200 |
| 0 | 201 <when value="single"> |
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202 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype "fastqsanger"" /> |
| 2 | 203 <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" /> |
| 0 | 204 </when> |
| 205 <when value="paired"> | |
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206 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> |
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207 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> |
| 2 | 208 <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" /> |
| 209 <conditional name="paired_options"> | |
| 210 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See "Alignment Options" section of Help below for information"> | |
| 211 <option value="no" selected="True">No</option> | |
| 212 <option value="yes">Yes</option> | |
| 213 </param> | |
| 214 <when value="yes"> | |
| 215 <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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216 <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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217 <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)"> |
| 2 | 218 <option value="--fr" selected="True">--fr</option> |
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219 <option value="--rf">--rf</option> |
| 2 | 220 <option value="--ff">--ff</option> |
| 221 </param> | |
| 222 <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"/> | |
| 223 <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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224 <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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225 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Allow 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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226 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Allow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/> |
| 2 | 227 </when> |
| 228 <when value="no"> | |
| 229 <!-- do nothing --> | |
| 230 </when> | |
| 231 </conditional> | |
| 232 </when> | |
| 233 <when value="paired_collection"> | |
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234 <param name="input_1" format="fastqsanger" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger"" /> |
| 2 | 235 <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" /> |
| 236 <conditional name="paired_options"> | |
| 237 <param name="paired_options_selector" type="select" label="Do you want to set paired-end options?" help="See "Alignment Options" section of Help below for information"> | |
| 238 <option value="no" selected="True">No</option> | |
| 239 <option value="yes">Yes</option> | |
| 240 </param> | |
| 241 <when value="yes"> | |
| 242 <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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243 <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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244 <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)"> |
| 2 | 245 <option value="--fr" selected="True">--fr</option> |
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246 <option value="--rf">--rf</option> |
| 2 | 247 <option value="--ff">--ff</option> |
| 248 </param> | |
| 249 <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"/> | |
| 250 <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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251 <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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252 <param name="no_contain" type="boolean" truevalue="--no-contain" falsevalue="" checked="False" label="Allow 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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253 <param name="no_overlap" type="boolean" truevalue="--no-overlap" falsevalue="" checked="False" label="Allow mate alignments to overlap" help="--no-overlap; If one mate alignment overlaps the other at all, consider that to be non-concordant. Default=False"/> |
| 2 | 254 </when> |
| 255 <when value="no"> | |
| 256 <!-- do nothing --> | |
| 257 </when> | |
| 258 </conditional> | |
| 0 | 259 </when> |
| 260 </conditional> | |
| 2 | 261 |
| 0 | 262 <!-- reference genome --> |
| 263 <conditional name="reference_genome"> | |
| 2 | 264 <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"> |
| 265 <option value="indexed">Use a built-in genome index</option> | |
| 266 <option value="history">Use a genome from the history and build index</option> | |
| 0 | 267 </param> |
| 268 <when value="indexed"> | |
| 2 | 269 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> |
| 0 | 270 <options from_data_table="bowtie2_indexes"> |
| 271 <filter type="sort_by" column="2"/> | |
| 272 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 273 </options> | |
| 274 </param> | |
| 275 </when> | |
| 276 <when value="history"> | |
| 2 | 277 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" /> |
| 0 | 278 </when> |
| 279 </conditional> | |
| 280 | |
| 2 | 281 <!-- read group settings --> |
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282 <expand macro="read_group_conditional" /> |
| 2 | 283 <conditional name="analysis_type"> |
| 284 <param name="analysis_type_selector" type="select" label="Select analysis mode"> | |
| 285 <option value="simple">1: Default setting only</option> | |
| 286 <option value="full">2: Full parameter list</option> | |
| 0 | 287 </param> |
| 2 | 288 <when value="simple"> |
| 289 <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."> | |
| 290 <option value="no_presets" selected="True">No, just use defaults</option> | |
| 291 <option value="--very-fast">Very fast end-to-end (--very-fast)</option> | |
| 292 <option value="--fast">Fast end-to-end (--fast)</option> | |
| 293 <option value="--sensitive">Sensitive end-to-end (--sensitive)</option> | |
| 294 <option value="--very-sensitive">Very sensitive end-to-end (--very-sensitive)</option> | |
| 295 <option value="--very-fast-local">Very fast local (--very-fast-local)</option> | |
| 296 <option value="--fast-local">Fast local (--fast-local)</option> | |
| 297 <option value="--sensitive-local">Sensitive local (--sensitive-local)</option> | |
| 298 <option value="--very-sensitive-local">Very sensitive local (--very-sensitive-local)</option> | |
| 0 | 299 </param> |
| 2 | 300 </when> |
| 301 <when value="full"> | |
| 302 <conditional name="input_options"> | |
| 303 <param name="input_options_selector" type="select" label="Do you want to tweak input options?" help="See "Input Options" section of Help below for information"> | |
| 304 <option value="yes">Yes</option> | |
| 305 <option value="no" selected="true">No</option> | |
| 306 </param> | |
| 307 <when value="yes"> | |
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308 <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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309 <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"/> |
| 2 | 310 <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"/> |
| 311 <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"/> | |
| 312 <param name="qv_encoding" type="select" display="radio" label="Select quality score encoding" help="See help below for more details"> | |
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313 <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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314 <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> |
| 2 | 315 </param> |
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316 <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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317 <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"/> |
| 2 | 318 </when> |
| 319 <when value="no"> | |
| 320 <!-- do nothing --> | |
| 321 </when> | |
| 322 </conditional> | |
| 323 <conditional name="alignment_options"> | |
| 324 <param name="alignment_options_selector" type="select" label="Do you want to tweak alignment options?" help="See "Alignment Options" section of Help below for information"> | |
| 325 <option value="yes">Yes</option> | |
| 326 <option value="no" selected="true">No</option> | |
| 327 </param> | |
| 328 <when value="yes"> | |
| 329 <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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330 <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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331 <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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332 <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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333 <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"/> |
| 2 | 334 <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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335 <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"/> |
| 2 | 336 <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"/> |
| 337 <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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338 <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"/> |
| 2 | 339 <conditional name="align_mode"> |
| 340 <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"> | |
| 341 <option value="end-to-end" selected="True">End to End (--end-to-end)</option> | |
| 342 <option value="local">Local (--local)</option> | |
| 343 </param> | |
| 344 <when value="end-to-end"> | |
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345 <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`"/> |
| 2 | 346 </when> |
| 347 <when value="local"> | |
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348 <param name="score_min_loc" type="text" value="G,20,8" label="Set a function governing the minimum alignment score needed for an alignment to be considered `valid` (i.e. good enough to report)" help="--score-min; This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. The default in `--end-to-end` mode is `L,-0.6,-0.6` and the default in `--local` mode is `G,20,8`"/> |
| 2 | 349 </when> |
| 350 </conditional> | |
| 351 </when> | |
| 352 <when value="no"> | |
| 353 <!-- do nothing --> | |
| 354 </when> | |
| 355 </conditional> | |
| 356 <conditional name="scoring_options"> | |
| 357 <param name="scoring_options_selector" type="select" label="Do you want to tweak scoring options?" help="See "Scoring Options" section of Help below for information"> | |
| 358 <option value="yes">Yes</option> | |
| 359 <option value="no" selected="true">No</option> | |
| 360 </param> | |
| 361 <when value="yes"> | |
| 362 <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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363 <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"/> |
| 2 | 364 <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"/> |
| 365 <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"/> | |
| 366 <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"/> | |
| 367 <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"/> | |
| 368 <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"/> | |
| 369 </when> | |
| 370 <when value="no"> | |
| 371 <!-- do nothing --> | |
| 372 </when> | |
| 373 </conditional> | |
| 374 <conditional name="reporting_options"> | |
| 375 <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 "Reporting Options" section of Help below for information on -k and -a options"> | |
| 376 <option value="no" selected="true">No, do not set</option> | |
| 377 <option value="k">Set -k option and enter -k value</option> | |
| 378 <option value="a">Set -a option</option> | |
| 379 </param> | |
| 380 <when value="no"> | |
| 381 <!-- do nothing --> | |
| 382 </when> | |
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383 <when value="k"> |
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384 <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"/> |
| 2 | 385 </when> |
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386 <when value="a"> |
| 2 | 387 <!-- do nothing here; set -a flag on the command line--> |
| 388 </when> | |
| 389 </conditional> | |
| 390 <conditional name="effort_options"> | |
| 391 <param name="effort_options_selector" type="select" label="Do you want to tweak effort options?" help="See "Effort Options" section of Help below for information"> | |
| 392 <option value="yes">Yes</option> | |
| 393 <option value="no" selected="true">No</option> | |
| 394 </param> | |
| 395 <when value="yes"> | |
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396 <param name="D" type="integer" value="15" min="0" label="Attempt that many consecutive seed extension attempts to `fail` before Bowtie 2 moves on, using the alignments found so far" help="-D; A seed extension `fails` if it does not yield a new best or a new second-best alignment. This limit is automatically adjusted up when -k or -a are specified. Default=15"/> |
| 2 | 397 <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"/> |
| 398 </when> | |
| 399 <when value="no"> | |
| 400 <!-- do nothing --> | |
| 401 </when> | |
| 402 </conditional> | |
| 0 | 403 |
| 2 | 404 <conditional name="sam_options"> |
| 405 <param name="sam_options_selector" type="select" label="Do you want to tweak SAM/BAM Options?" help="See "Output Options" section of Help below for information"> | |
| 406 <option value="yes">Yes</option> | |
| 407 <option value="no" selected="true">No</option> | |
| 408 </param> | |
| 409 <when value="yes"> | |
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410 <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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411 <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/> |
| 2 | 412 </when> |
| 413 <when value="no"> | |
| 414 <!-- do nothing --> | |
| 415 </when> | |
| 416 </conditional> | |
| 417 <conditional name="other_options"> | |
| 418 <param name="other_options_selector" type="select" label="Do you want to tweak Other Options?" help="See "Other Options" section of Help below for information"> | |
| 419 <option value="yes">Yes</option> | |
| 420 <option value="no" selected="true">No</option> | |
| 421 </param> | |
| 422 <when value="yes"> | |
| 423 <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"/> | |
| 424 <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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425 <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/> |
| 2 | 426 </when> |
| 427 <when value="no"> | |
| 428 <!-- do nothing --> | |
| 429 </when> | |
| 430 </conditional> | |
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431 <param name="sam_opt" type="boolean" truevalue="true" falsevalue="false" label="Would you like the output to be a SAM file" help="By default, the output from this Bowtie2 wrapper is a sorted BAM file."/> |
| 0 | 432 </when> |
| 433 </conditional> | |
| 434 </inputs> | |
| 435 | |
| 436 <!-- define outputs --> | |
| 2 | 437 |
| 0 | 438 <outputs> |
| 2 | 439 |
| 0 | 440 <data format="fastqsanger" name="output_unaligned_reads_l" label="${tool.name} on ${on_string}: unaligned reads (L)" > |
| 2 | 441 <filter>library['unaligned_file'] is True</filter> |
| 0 | 442 <actions> |
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443 <conditional name="library.type"> |
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444 <when value="single"> |
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445 <action type="format"> |
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446 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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447 </action> |
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448 </when> |
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449 <when value="paired"> |
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450 <action type="format"> |
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451 <option type="from_param" name="library.input_1" param_attribute="ext" /> |
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452 </action> |
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453 </when> |
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454 <when value="paired_collection"> |
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455 <action type="format"> |
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456 <option type="from_param" name="library.input_1" param_attribute="forward.ext" /> |
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457 </action> |
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458 </when> |
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459 </conditional> |
| 0 | 460 </actions> |
| 461 </data> | |
| 462 <data format="fastqsanger" name="output_unaligned_reads_r" label="${tool.name} on ${on_string}: unaligned reads (R)"> | |
| 2 | 463 <filter>( library['type'] == "paired" or library['type'] == "paired_collection" ) and library['unaligned_file'] is True</filter> |
| 0 | 464 <actions> |
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465 <conditional name="library.type"> |
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466 <when value="paired"> |
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467 <action type="format"> |
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468 <option type="from_param" name="library.input_2" param_attribute="ext" /> |
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469 </action> |
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470 </when> |
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471 <when value="paired_collection"> |
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472 <action type="format"> |
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473 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> |
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474 </action> |
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475 </when> |
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476 </conditional> |
| 0 | 477 </actions> |
| 478 </data> | |
| 2 | 479 |
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480 <data format="bam" name="output" label="${tool.name} on ${on_string}: aligned reads (sorted BAM)"> |
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481 <filter>analysis_type['analysis_type_selector'] == "simple" or analysis_type['sam_opt'] is False</filter> |
| 0 | 482 <actions> |
| 483 <conditional name="reference_genome.source"> | |
| 484 <when value="indexed"> | |
| 485 <action type="metadata" name="dbkey"> | |
| 486 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> | |
| 487 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> | |
| 488 <filter type="param_value" ref="reference_genome.index" column="0"/> | |
| 489 </option> | |
| 490 </action> | |
| 491 </when> | |
| 492 <when value="history"> | |
| 493 <action type="metadata" name="dbkey"> | |
| 494 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> | |
| 495 </action> | |
| 496 </when> | |
| 497 </conditional> | |
| 498 </actions> | |
| 499 </data> | |
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500 |
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501 <data format="sam" name="output_sam" label="${tool.name} on ${on_string}: aligned reads (SAM)"> |
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502 <filter>analysis_type['analysis_type_selector'] == "full" and analysis_type['sam_opt'] is True</filter> |
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503 <actions> |
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504 <conditional name="reference_genome.source"> |
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505 <when value="indexed"> |
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506 <action type="metadata" name="dbkey"> |
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507 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0"> |
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508 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> |
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509 <filter type="param_value" ref="reference_genome.index" column="0"/> |
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510 </option> |
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511 </action> |
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512 </when> |
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513 <when value="history"> |
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514 <action type="metadata" name="dbkey"> |
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515 <option type="from_param" name="reference_genome.own_file" param_attribute="dbkey" /> |
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516 </action> |
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517 </when> |
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518 </conditional> |
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519 </actions> |
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520 </data> |
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521 |
| 0 | 522 </outputs> |
| 523 | |
| 524 <tests> | |
| 525 <test> | |
| 526 <!-- basic test on single paired default run --> | |
| 2 | 527 <param name="type" value="paired"/> |
| 0 | 528 <param name="selection" value="no"/> |
| 2 | 529 <param name="paired_options_selector" value="no"/> |
| 0 | 530 <param name="unaligned_file" value="false"/> |
| 2 | 531 <param name="analysis_type_selector" value="simple"/> |
| 0 | 532 <param name="source" value="history" /> |
| 2 | 533 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
| 534 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> | |
| 535 <param name="own_file" value="bowtie2-ref.fasta" /> | |
| 536 <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/> | |
| 0 | 537 </test> |
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538 <test> |
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539 <!-- basic test on single paired default run --> |
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540 <param name="type" value="paired"/> |
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541 <param name="selection" value="no"/> |
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542 <param name="paired_options_selector" value="no"/> |
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543 <param name="unaligned_file" value="false"/> |
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544 <param name="analysis_type_selector" value="simple"/> |
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545 <param name="rg_selector" value="set"/> |
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546 <param name="ID" value="rg1"/> |
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547 <param name="PL" value="CAPILLARY"/> |
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548 <param name="source" value="history" /> |
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549 <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/> |
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550 <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/> |
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551 <param name="own_file" value="bowtie2-ref.fasta" /> |
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552 <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/> |
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553 </test> |
| 0 | 554 </tests> |
| 555 | |
| 556 <help> | |
| 2 | 557 |
| 0 | 558 **Bowtie2 Overview** |
| 559 | |
| 2 | 560 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. |
| 561 Majority of information in this page is derived from an excellent `Bowtie2 manual`_ written by Ben Langmead. | |
| 562 | |
| 563 .. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/ | |
| 564 .. _`Bowtie2 manual`: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml | |
| 565 .. _`BAM format`: http://samtools.github.io/hts-specs/SAMv1.pdf | |
| 566 | |
| 567 ----- | |
| 0 | 568 |
| 2 | 569 **Selecting reference genomes for Bowtie2** |
| 570 | |
| 571 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 | 572 |
| 2 | 573 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. |
| 574 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. | |
| 575 | |
| 576 If your genome of interest is not listed here you have two choices: | |
| 577 | |
| 578 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 | |
| 579 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 | 580 |
| 581 ------ | |
| 582 | |
| 2 | 583 .. class:: infomark |
| 584 | |
| 585 **Bowtie2 options** | |
| 586 | |
| 587 Galaxy wrapper for Bowtie2 implements most but not all options available through the command line. Supported options are described below. | |
| 588 | |
| 589 ----- | |
| 590 | |
| 0 | 591 **Inputs** |
| 592 | |
| 593 Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files. | |
| 594 | |
| 595 ------ | |
| 596 | |
| 2 | 597 **Input options**:: |
| 598 | |
| 599 -s/--skip <int> | |
| 600 Skip (i.e. do not align) the first `<int>` reads or pairs in the input. | |
| 601 | |
| 602 -u/--qupto <int> | |
| 603 Align the first `<int>` reads or read pairs from the input (after the | |
| 604 `-s`/`--skip` reads or pairs have been skipped), then stop. Default: no limit. | |
| 605 | |
| 606 -5/--trim5 <int> | |
| 607 Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0). | |
| 0 | 608 |
| 2 | 609 -3/--trim3 <int> |
| 610 Trim `<int>` bases from 3' (right) end of each read before alignment (default: 0). | |
| 611 | |
| 612 --phred33 | |
| 613 Input qualities are ASCII chars equal to the Phred quality plus 33. This is | |
| 614 also called the "Phred+33" encoding, which is used by the very latest Illumina | |
| 615 pipelines. | |
| 616 | |
| 617 --phred64 | |
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618 Input qualities are ASCII chars equal to the Phred quality plus 64. This is |
| 2 | 619 also called the "Phred+64" encoding. |
| 0 | 620 |
| 2 | 621 --solexa-quals |
| 622 Convert input qualities from Solexa Phred quality (which can be negative) to | |
| 623 Phred Phred quality (which can't). This scheme was used in older Illumina GA | |
| 624 Pipeline versions (prior to 1.3). Default: off. | |
| 625 | |
| 626 --int-quals | |
| 627 Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`.... | |
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628 Integers are treated as being on the Phred quality scale unless |
| 2 | 629 `--solexa-quals` is also specified. Default: off. |
| 630 | |
| 631 ------ | |
| 632 | |
| 633 **Presets in `--end-to-end` mode**:: | |
| 634 | |
| 635 --very-fast | |
| 636 Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50` | |
| 637 | |
| 638 --fast | |
| 639 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50` | |
| 640 | |
| 641 --sensitive | |
| 642 Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in `--end-to-end` mode) | |
| 643 | |
| 644 --very-sensitive | |
| 645 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
| 0 | 646 |
| 647 ------ | |
| 648 | |
| 2 | 649 **Presets options in `--local` mode**:: |
| 0 | 650 |
| 2 | 651 --very-fast-local |
| 652 Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00` | |
| 0 | 653 |
| 2 | 654 --fast-local |
| 655 Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75` | |
| 0 | 656 |
| 2 | 657 --sensitive-local |
| 658 Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in `--local` mode) | |
| 0 | 659 |
| 2 | 660 --very-sensitive-local |
| 661 Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` | |
| 662 | |
| 0 | 663 ------ |
| 664 | |
| 2 | 665 **Alignment options**:: |
| 666 | |
| 667 -N <int> | |
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668 Sets the number of mismatches to allowed in a seed alignment during multiseed |
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669 alignment. Can be set to 0 or 1. Setting this higher makes alignment slower |
| 2 | 670 (often much slower) but increases sensitivity. Default: 0. |
| 671 | |
| 672 -L <int> | |
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673 Sets the length of the seed substrings to align during multiseed alignment. |
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674 Smaller values make alignment slower but more sensitive. Default: the |
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675 `--sensitive` preset is used by default, which sets `-L` to 22 in |
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676 `--end-to-end` mode and to 20 in `--local` mode. |
| 2 | 677 |
| 678 -i <func> | |
| 679 Sets a function governing the interval between seed substrings to use during | |
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680 multiseed alignment. For instance, if the read has 30 characers, and seed |
| 2 | 681 length is 10, and the seed interval is 6, the seeds extracted will be: |
| 682 | |
| 683 Read: TAGCTACGCTCTACGCTATCATGCATAAAC | |
| 684 Seed 1 fw: TAGCTACGCT | |
| 685 Seed 1 rc: AGCGTAGCTA | |
| 686 Seed 2 fw: CGCTCTACGC | |
| 687 Seed 2 rc: GCGTAGAGCG | |
| 688 Seed 3 fw: ACGCTATCAT | |
| 689 Seed 3 rc: ATGATAGCGT | |
| 690 Seed 4 fw: TCATGCATAA | |
| 691 Seed 4 rc: TTATGCATGA | |
| 692 | |
| 693 Since it's best to use longer intervals for longer reads, this parameter sets | |
| 694 the interval as a function of the read length, rather than a single | |
| 695 one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the | |
| 696 interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. | |
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697 If the function returns a result less than |
| 2 | 698 1, it is rounded up to 1. Default: the `--sensitive` preset is used by |
| 699 default, which sets `-i` to `S,1,1.15` in `--end-to-end` mode to `-i S,1,0.75` | |
| 700 in `--local` mode. | |
| 701 | |
| 702 --n-ceil <func> | |
| 703 Sets a function governing the maximum number of ambiguous characters (usually | |
| 704 `N`s and/or `.`s) allowed in a read as a function of read length. For instance, | |
| 705 specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, | |
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706 where x is the read length. Reads exceeding this ceiling are filtered out. |
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707 Default: `L,0,0.15`. |
| 2 | 708 |
| 709 --dpad <int> | |
| 710 "Pads" dynamic programming problems by `<int>` columns on either side to allow | |
| 711 gaps. Default: 15. | |
| 712 | |
| 713 --gbar <int> | |
| 714 Disallow gaps within `<int>` positions of the beginning or end of the read. | |
| 715 Default: 4. | |
| 716 | |
| 717 --ignore-quals | |
| 718 When calculating a mismatch penalty, always consider the quality value at the | |
| 719 mismatched position to be the highest possible, regardless of the actual value. | |
| 720 I.e. input is treated as though all quality values are high. This is also the | |
| 721 default behavior when the input doesn't specify quality values (e.g. in `-f`, | |
| 722 `-r`, or `-c` modes). | |
| 0 | 723 |
| 2 | 724 --nofw/--norc |
| 725 If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to | |
| 726 the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will | |
| 727 not attempt to align unpaired reads against the reverse-complement (Crick) | |
| 728 reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the | |
| 729 fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those | |
| 730 paired-end configurations corresponding to fragments from the reverse-complement | |
| 731 (Crick) strand. Default: both strands enabled. | |
| 732 | |
| 733 --no-1mm-upfront | |
| 734 By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch | |
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735 end-to-end alignment for the read *before* trying the multiseed heuristic. Such |
| 2 | 736 alignments can be found very quickly, and many short read alignments have exact or |
| 737 near-exact end-to-end alignments. However, this can lead to unexpected | |
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738 alignments when the user also sets options governing the multiseed heuristic, |
| 2 | 739 like `-L` and `-N`. For instance, if the user specifies `-N 0` and `-L` equal |
| 740 to the length of the read, the user will be surprised to find 1-mismatch alignments | |
| 741 reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end | |
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742 alignments before using the multiseed heuristic, which leads to the expected |
| 2 | 743 behavior when combined with options such as `-L` and `-N`. This comes at the |
| 744 expense of speed. | |
| 745 | |
| 746 --end-to-end | |
| 747 In this mode, Bowtie 2 requires that the entire read align from one end to the | |
| 748 other, without any trimming (or "soft clipping") of characters from either end. | |
| 749 The match bonus `--ma` always equals 0 in this mode, so all alignment scores | |
| 750 are less than or equal to 0, and the greatest possible alignment score is 0. | |
| 751 This is mutually exclusive with `--local`. `--end-to-end` is the default mode. | |
| 0 | 752 |
| 2 | 753 --local |
| 754 In this mode, Bowtie 2 does not require that the entire read align from one end | |
| 755 to the other. Rather, some characters may be omitted ("soft clipped") from the | |
| 756 ends in order to achieve the greatest possible alignment score. The match bonus | |
| 757 `--ma` is used in this mode, and the best possible alignment score is equal to | |
| 758 the match bonus (`--ma`) times the length of the read. Specifying `--local` | |
| 759 and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying | |
| 760 the local version of the preset (`--very-fast-local`). This is mutually | |
| 761 exclusive with `--end-to-end`. `--end-to-end` is the default mode. | |
| 762 | |
| 763 ----- | |
| 764 | |
| 765 **Scoring options**:: | |
| 766 | |
| 767 --ma <int> | |
| 768 Sets the match bonus. In `--local` mode `<int>` is added to the alignment | |
| 769 score for each position where a read character aligns to a reference character | |
| 770 and the characters match. Not used in `--end-to-end` mode. Default: 2. | |
| 771 | |
| 772 --mp MX,MN | |
| 773 Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A | |
| 774 number less than or equal to `MX` and greater than or equal to `MN` is | |
| 775 subtracted from the alignment score for each position where a read character | |
| 776 aligns to a reference character, the characters do not match, and neither is an | |
| 777 `N`. If `--ignore-quals` is specified, the number subtracted quals `MX`. | |
| 778 Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` | |
| 779 where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2. | |
| 780 | |
| 781 --np <int> | |
| 782 Sets penalty for positions where the read, reference, or both, contain an | |
| 783 ambiguous character such as `N`. Default: 1. | |
| 784 | |
| 785 --rdg <int1>,<int2> | |
| 786 Sets the read gap open (`<int1>`) and extend (`<int2>`) penalties. A read gap of | |
| 787 length N gets a penalty of `<int1>` + N * `<int2>`. Default: 5, 3. | |
| 788 | |
| 789 --rfg <int1>,<int2> | |
| 790 Sets the reference gap open (`<int1>`) and extend (`<int2>`) penalties. A | |
| 791 reference gap of length N gets a penalty of `<int1>` + N * `<int2>`. Default: | |
| 792 5, 3. | |
| 0 | 793 |
| 2 | 794 --score-min <func> |
| 795 Sets a function governing the minimum alignment score needed for an alignment to | |
| 796 be considered "valid" (i.e. good enough to report). This is a function of read | |
| 797 length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` | |
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798 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 | 799 the default in `--local` mode is `G,20,8`. |
| 800 | |
| 801 ----- | |
| 802 | |
| 803 **Reporting options**:: | |
| 804 | |
| 805 -k <int> | |
| 806 By default, `bowtie2` searches for distinct, valid alignments for each read. | |
| 807 When it finds a valid alignment, it continues looking for alignments that are | |
| 808 nearly as good or better. The best alignment found is reported (randomly | |
| 809 selected from among best if tied). Information about the best alignments is | |
| 810 used to estimate mapping quality and to set SAM optional fields, such as | |
| 811 `AS:i` and `XS:i`. | |
| 812 | |
| 813 When `-k` is specified, however, `bowtie2` behaves differently. Instead, it | |
| 814 searches for at most `<int>` distinct, valid alignments for each read. The | |
| 815 search terminates when it can't find more distinct valid alignments, or when it | |
| 816 finds `<int>`, whichever happens first. All alignments found are reported in | |
| 817 descending order by alignment score. The alignment score for a paired-end | |
| 818 alignment equals the sum of the alignment scores of the individual mates. Each | |
| 819 reported read or pair alignment beyond the first has the SAM 'secondary' bit | |
| 820 (which equals 256) set in its FLAGS field. For reads that have more than | |
| 821 `<int>` distinct, valid alignments, `bowtie2` does not guarantee that the | |
| 822 `<int>` alignments reported are the best possible in terms of alignment score. | |
| 823 `-k` is mutually exclusive with `-a`. | |
| 0 | 824 |
| 2 | 825 Note: Bowtie 2 is not designed with large values for `-k` in mind, and when |
| 826 aligning reads to long, repetitive genomes large `-k` can be very, very slow. | |
| 827 | |
| 828 -a | |
| 829 Like `-k` but with no upper limit on number of alignments to search for. `-a` | |
| 830 is mutually exclusive with `-k`. | |
| 831 | |
| 832 Note: Bowtie 2 is not designed with `-a` mode in mind, and when | |
| 833 aligning reads to long, repetitive genomes this mode can be very, very slow. | |
| 834 | |
| 835 ----- | |
| 836 | |
| 837 **Effort options**:: | |
| 838 | |
| 839 -D <int> | |
| 840 Up to `<int>` consecutive seed extension attempts can "fail" before Bowtie 2 | |
| 841 moves on, using the alignments found so far. A seed extension "fails" if it | |
| 842 does not yield a new best or a new second-best alignment. This limit is | |
| 843 automatically adjusted up when -k or -a are specified. Default: 15. | |
| 844 | |
| 845 -R <int> | |
| 846 `<int>` is the maximum number of times Bowtie 2 will "re-seed" reads with | |
| 847 repetitive seeds. When "re-seeding," Bowtie 2 simply chooses a new set of reads | |
| 848 (same length, same number of mismatches allowed) at different offsets and | |
| 849 searches for more alignments. A read is considered to have repetitive seeds if | |
| 850 the total number of seed hits divided by the number of seeds that aligned at | |
| 851 least once is greater than 300. Default: 2. | |
| 852 | |
| 853 ----- | |
| 854 | |
| 855 **Paired-end options**:: | |
| 0 | 856 |
| 2 | 857 -I/--minins <int> |
| 858 The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is | |
| 859 specified and a paired-end alignment consists of two 20-bp alignments in the | |
| 860 appropriate orientation with a 20-bp gap between them, that alignment is | |
| 861 considered valid (as long as `-X` is also satisfied). A 19-bp gap would not | |
| 862 be valid in that case. If trimming options `-3` or `-5` are also used, the | |
| 863 `-I` constraint is applied with respect to the untrimmed mates. | |
| 864 | |
| 865 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
| 866 run. This is because larger differences bewteen `-I` and `-X` require that | |
| 867 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
| 868 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
| 869 efficient. | |
| 870 | |
| 871 Default: 0 (essentially imposing no minimum) | |
| 872 | |
| 873 -X/--maxins <int> | |
| 874 The maximum fragment length for valid paired-end alignments. E.g. if `-X 100` | |
| 875 is specified and a paired-end alignment consists of two 20-bp alignments in the | |
| 876 proper orientation with a 60-bp gap between them, that alignment is considered | |
| 877 valid (as long as `-I` is also satisfied). A 61-bp gap would not be valid in | |
| 878 that case. If trimming options `-3` or `-5` are also used, the `-X` | |
| 879 constraint is applied with respect to the untrimmed mates, not the trimmed | |
| 880 mates. | |
| 881 | |
| 882 The larger the difference between `-I` and `-X`, the slower Bowtie 2 will | |
| 883 run. This is because larger differences bewteen `-I` and `-X` require that | |
| 884 Bowtie 2 scan a larger window to determine if a concordant alignment exists. | |
| 885 For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very | |
| 886 efficient. | |
| 887 | |
| 888 Default: 500. | |
| 0 | 889 |
| 2 | 890 --fr/--rf/--ff |
| 891 The upstream/downstream mate orientations for a valid paired-end alignment | |
| 892 against the forward reference strand. E.g., if `--fr` is specified and there is | |
| 893 a candidate paired-end alignment where mate 1 appears upstream of the reverse | |
| 894 complement of mate 2 and the fragment length constraints (`-I` and `-X`) are | |
| 895 met, that alignment is valid. Also, if mate 2 appears upstream of the reverse | |
| 896 complement of mate 1 and all other constraints are met, that too is valid. | |
| 897 `--rf` likewise requires that an upstream mate1 be reverse-complemented and a | |
| 898 downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1 | |
| 899 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate | |
| 900 for Illumina's Paired-end Sequencing Assay). | |
| 901 | |
| 902 --no-mixed | |
| 903 By default, when `bowtie2` cannot find a concordant or discordant alignment for | |
| 904 a pair, it then tries to find alignments for the individual mates. This option | |
| 905 disables that behavior. | |
| 0 | 906 |
| 2 | 907 --no-discordant |
| 908 By default, `bowtie2` looks for discordant alignments if it cannot find any | |
| 909 concordant alignments. A discordant alignment is an alignment where both mates | |
| 910 align uniquely, but that does not satisfy the paired-end constraints | |
| 911 (`--fr`/`--rf`/`--ff`, `-I`, `-X`). This option disables that behavior. | |
| 912 | |
| 913 --dovetail | |
| 914 If the mates "dovetail", that is if one mate alignment extends past the | |
| 915 beginning of the other such that the wrong mate begins upstream, consider that | |
|
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916 to be concordant. Default: mates cannot dovetail in a concordant alignment. |
| 2 | 917 |
| 918 --no-contain | |
| 919 If one mate alignment contains the other, consider that to be non-concordant. | |
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920 Default: a mate can contain the other in a concordant alignment. |
| 2 | 921 |
| 922 --no-overlap | |
| 923 If one mate alignment overlaps the other at all, consider that to be | |
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924 non-concordant. Default: mates can overlap in a concordant alignment. |
| 2 | 925 |
| 0 | 926 ------ |
| 927 | |
| 2 | 928 **SAM options**:: |
| 0 | 929 |
| 2 | 930 --rg-id <text> |
| 931 Set the read group ID to `<text>`. This causes the SAM `@RG` header line to be | |
| 932 printed, with `<text>` as the value associated with the `ID:` tag. It also | |
| 933 causes the `RG:Z:` extra field to be attached to each SAM output record, with | |
| 934 value set to `<text>`. | |
| 0 | 935 |
| 2 | 936 --rg <text> |
| 937 Add `<text>` (usually of the form `TAG:VAL`, e.g. `SM:Pool1`) as a field on the | |
| 938 `@RG` header line. Note: in order for the `@RG` line to appear, `--rg-id` | |
|
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939 must also be specified. This is because the `ID` tag is required by the SAM |
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940 Specification. Specify `--rg` multiple times to set multiple fields. See the |
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941 SAM Specification for details about what fields are legal. |
| 0 | 942 |
| 2 | 943 --omit-sec-seq |
| 944 When printing secondary alignments, Bowtie 2 by default will write out the `SEQ` | |
| 945 and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterix | |
| 946 in those fields instead. | |
| 947 | |
| 948 ----- | |
| 0 | 949 |
| 2 | 950 **Other options**:: |
| 0 | 951 |
| 2 | 952 --reorder |
| 953 Guarantees that output SAM records are printed in an order corresponding to the | |
| 954 order of the reads in the original input file, even when `-p` is set greater | |
| 955 than 1. Specifying `--reorder` and setting `-p` greater than 1 causes Bowtie | |
| 956 2 to run somewhat slower and use somewhat more memory then if `--reorder` were | |
| 957 not specified. Has no effect if `-p` is set to 1, since output order will | |
| 958 naturally correspond to input order in that case. | |
| 0 | 959 |
| 2 | 960 --seed <int> |
| 961 Use `<int>` as the seed for pseudo-random number generator. Default: 0. | |
| 0 | 962 |
| 2 | 963 --non-deterministic |
| 964 Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It | |
| 965 seeds the generator with a number derived from (a) the read name, (b) the | |
| 966 nucleotide sequence, (c) the quality sequence, (d) the value of the `--seed` | |
| 967 option. This means that if two reads are identical (same name, same | |
| 968 nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s) | |
| 969 for both, even if there was ambiguity. When `--non-deterministic` is specified, | |
| 970 Bowtie 2 re-initializes its pseudo-random generator for each read using the | |
| 971 current time. This means that Bowtie 2 will not necessarily report the same | |
| 972 alignment for two identical reads. This is counter-intuitive for some users, | |
| 973 but might be more appropriate in situations where the input consists of many | |
| 974 identical reads. | |
| 0 | 975 |
| 976 </help> | |
| 2 | 977 <citations> |
| 978 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> | |
| 979 <citation type="doi">10.1038/nmeth.1923</citation> | |
| 980 </citations> | |
| 0 | 981 </tool> |