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1 <tool id="trim_galore" name="Trim Galore" version="0.2.4.0">
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2 <!-- Wrapper compatible with Trim Galore version 0.2.4.0 -->
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3 <description>adaptive quality and adapter trimmer</description>
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4 <version_command interpreter="perl">trim_galore --version</version_command>
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5 <requirements>
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6 <requirement type="package" version="1.1">cutadapt</requirement>
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7 <requirement type="package" version="0.10.1">fastqc</requirement>
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8 </requirements>
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9 <command interpreter="perl">
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10 #from glob import glob
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11 #import tempfile, os
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12
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13 trim_galore
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14
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15 ##
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16 ## Input parameters
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17 ##
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18
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19
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20 #if $params.settingsType == "custom":
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21
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22 $params.fastqc
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23 ## default 20
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24 --quality $params.quality
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25 ## default 'AGATCGGAAGAGC'
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26 #if $params.adapter.strip() != '':
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27 --adapter $params.adapter
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28 #end if
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29 ## default 1
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30 --stringency $params.stringency
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31
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32 ## default 0.1
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33 -e $params.error_rate
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34
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35 ## default 20
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36 --length $params.min_length
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37
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38 #if $params.retain_unpaired.settingsType == "retain_unpaired_output":
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39 --retain_unpaired
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40 --length_1 $params.retain_unpaired.length_1
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41 --length_2 $params.retain_unpaired.length_2
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42 #end if
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43
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44 #end if
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45
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46 ##
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47 ## RBBS specific options.
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48 ##
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49
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50 #if $rrbs.settingsType == "custom":
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51
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52 $rrbs
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53 $non_directional
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54
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55 #end if
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56
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57 ##
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58 ## Creating a temporary directory where trim_galore will store all result files
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59 ##
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60
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61 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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62
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63 --output_dir $temp_dir
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64 --suppress_warn
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65
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66
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67 #if $singlePaired.sPaired == "single":
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68
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69 #if $singlePaired.input_singles.ext == "fastqillumina":
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70 --phred64
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71 #elif $singlePaired.input_singles.ext == "fastqsanger":
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72 --phred33
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73 #end if
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74
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75 #if $params.settingsType == "custom":
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76 #if not $params.report:
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77 --no_report_file
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78 #end if
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79 #end if
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80
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81 ## input sequence
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82 $singlePaired.input_singles
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83 #else:
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84 --paired
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85 #if $singlePaired.input_mate1.ext == "fastqillumina":
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86 --phred64
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87 #elif $singlePaired.input_mate1.ext == "fastqsanger":
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88 --phred33
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89 #end if
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90
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91 $singlePaired.trim1
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92 #if $singlePaired.adapter2.strip() != '':
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93 --adapter2 $singlePaired.adapter2
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94 #end if
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95
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96 #if $params.settingsType == "custom":
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97 #if not $params.report:
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98 --no_report_file
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99 #end if
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100 #end if
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101
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102 ## input sequences
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103 $singlePaired.input_mate1
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104 $singlePaired.input_mate2
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105
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106 #end if
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107
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108 &&
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109
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110 ##
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111 ## Trim Galore! run is finished. Move the result files to the proper place
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112 ##
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113
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114
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115 #if $singlePaired.sPaired == "single":
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116 #set $single_end_path = os.path.join($temp_dir, os.path.basename(str($singlePaired.input_singles)) + '_trimmed.fq')
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117 mv $single_end_path $trimmed_reads_single;
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118
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119 #if $params.settingsType == "custom":
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120 #if $params.report:
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121 #set $report_path = os.path.join($temp_dir, os.path.basename(str($singlePaired.input_singles)) + '_trimming_report.txt')
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122 mv $report_path $report_file;
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123 #end if
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124 #end if
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125
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126 #else:
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127 #set $paired_end_path_1 = os.path.join($temp_dir, os.path.basename(str($singlePaired.input_mate1)) + '_val_1.fq')
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128 #set $paired_end_path_2 = os.path.join($temp_dir, os.path.basename(str($singlePaired.input_mate2)) + '_val_2.fq')
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129 mv $paired_end_path_1 $trimmed_reads_pair1;
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130 mv $paired_end_path_2 $trimmed_reads_pair2;
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131
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132 #if $params.settingsType == "custom":
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133 #if $params.retain_unpaired.settingsType == "retain_unpaired_output":
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134 #set $unpaired_path_1 = os.path.join($temp_dir, os.path.basename(str($singlePaired.input_mate1)) + '_unpaired_1.fq')
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135 #set $unpaired_path_2 = os.path.join($temp_dir, os.path.basename(str($singlePaired.input_mate2)) + '_unpaired_2.fq')
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136 mv $unpaired_path_1 $unpaired_reads_1;
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137 mv $unpaired_path_2 $unpaired_reads_2;
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138 #end if
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139
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140 #if $params.report:
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141 #set $report_path = os.path.join($temp_dir, os.path.basename(str($singlePaired.input_mate1)) + '_trimming_report.txt')
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142 mv $report_path $report_file;
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143 #end if
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144
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145 #end if
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146 #end if
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147
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148 ## delete the temp_dir
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149 ##rm -rf $temp_dir;
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150
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151 </command>
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152 <inputs>
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153
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154 <!-- Input Parameters -->
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155 <conditional name="singlePaired">
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156 <param name="sPaired" type="select" label="Is this library mate-paired?">
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157 <option value="single">Single-end</option>
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158 <option value="paired">Paired-end</option>
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159 </param>
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160 <when value="single">
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161 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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162 </when>
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163 <when value="paired">
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164 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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165 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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166 <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
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167 <param name="adapter2" type="text" value="" label="Optional adapter sequence to be trimmed off read 2">
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168 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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169 </param>
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170 </when>
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171 </conditional>
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172
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173
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174 <conditional name="params">
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175 <param name="settingsType" type="select" label="Trim galore! advanced settings" help="You can use the default settings or set custom values for any of Trim Galore's parameters.">
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176 <option value="default">Use Defaults</option>
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177 <option value="custom">Full parameter list</option>
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178 </param>
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179 <when value="default" />
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180 <!-- Full/advanced params. -->
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181 <when value="custom">
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182 <param name="fastqc" type="boolean" truevalue="--fastqc" falsevalue="" checked="False" label="Run FastQC in the default mode on the FastQ file once trimming is complete" help="" />
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183 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal." help="For more information please see below." />
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184 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed">
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185 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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186 </param>
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187 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
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188 <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
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189 <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length INT" />
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190
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191 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
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192
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193 <conditional name="retain_unpaired">
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194 <param name="settingsType" type="select" label="specify if you would like to retain unpaired reads">
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195 <option value="no_output">Do not output unpaired reads</option>
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196 <option value="retain_unpaired_output">Output unpaired reads</option>
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197 </param>
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198 <when value="no_output" />
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199 <!-- Output params. -->
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200 <when value="retain_unpaired_output">
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201 <param name="length_1" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 1 to be written" />
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202 <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" />
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203 </when> <!-- output -->
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204 </conditional> <!-- retain_unpaired -->
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205
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206 </when> <!-- full -->
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207 </conditional> <!-- params -->
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208
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209 <conditional name="rrbs">
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210 <param name="settingsType" type="select" label="RRBS specific settings">
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211 <option value="default">Use Defaults</option>
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212 <option value="custom">Full parameter list</option>
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213 </param>
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214 <when value="default" />
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215 <!-- Full/advanced params. -->
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216 <when value="custom">
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217 <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True" label="Specifies that the input file was an MspI digested RRBS sample" />
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218 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False" label="Selecting this option for non-directional RRBS libraries" />
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219 </when> <!-- full -->
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220 </conditional> <!-- params -->
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221
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222 </inputs>
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223 <outputs>
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224
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225 <data format="fastq" name="trimmed_reads_single" label="${tool.name} on ${on_string}: trimmed reads">
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226 <filter>singlePaired['sPaired'] == "single"</filter>
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227 <actions>
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228 <action type="format">
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229 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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230 </action>
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231 </actions>
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232 </data>
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233
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234 <data format="fastq" name="trimmed_reads_pair1" label="${tool.name} on ${on_string}: trimmed reads pair 1">
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235 <filter>singlePaired['sPaired'] == "paired"</filter>
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236 <actions>
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237 <action type="format">
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238 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
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239 </action>
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240 </actions>
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241 </data>
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242
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243 <data format="fastq" name="trimmed_reads_pair2" label="${tool.name} on ${on_string}: trimmed reads pair 2">
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244 <filter>singlePaired['sPaired'] == "paired"</filter>
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245 <actions>
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246 <action type="format">
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247 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
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248 </action>
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249 </actions>
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250 </data>
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251
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252 <data format="fastq" name="unpaired_reads_1" label="${tool.name} on ${on_string}: unpaired reads (1)">
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253 <filter>
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254 ((
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255 params['settingsType'] == "custom" and
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256 params['retain_unpaired']['settingsType'] == "retain_unpaired_output"
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257 ))
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258 </filter>
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259 <actions>
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260 <action type="format">
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261 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
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262 </action>
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263 </actions>
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264 </data>
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265
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266 <data format="fastq" name="unpaired_reads_2" label="${tool.name} on ${on_string}: unpaired reads (2)">
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267 <filter>
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268 ((
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269 params['settingsType'] == "custom" and
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270 params['retain_unpaired']['settingsType'] == "retain_unpaired_output"
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271 ))
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272 </filter>
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273 <actions>
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274 <action type="format">
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275 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
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276 </action>
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277 </actions>
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278 </data>
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279
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280 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
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281 <filter>
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282 ((
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283 params['settingsType'] == "custom" and
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284 params['report'] == True
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285 ))
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286 </filter>
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287 </data>
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288
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289 </outputs>
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290 <tests>
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291 </tests>
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292
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293 <help>
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294
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295 **What it does**
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296
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297 TrimGalore!_ is a wrapper script that makes use of the publically available
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298 adapter trimming tool Cutadapt and FastQC for optional quality control once
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299 the trimming process has completed.
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300
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301
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302 .. _TrimGalore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
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303
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304
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305 It is developed by Krueger F at the Babraham Institute.
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306
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307 ------
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308
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309 **Know what you are doing**
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310
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311 .. class:: warningmark
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312
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313 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
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314
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315 .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
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316
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317 ------
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318
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319 **Input formats**
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320
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321 Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files.
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322
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323 ------
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324
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325 **A Note on Built-in Reference Genomes**
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326
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327 The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
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328
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329 ------
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330
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331 The final output of Bismark is in SAM format by default.
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332
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333 **Outputs**
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334
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335 The output is in SAM format, and has the following columns::
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336
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337 Column Description
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338 -------- --------------------------------------------------------
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339 1 QNAME seq-ID
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340 2 FLAG this flag tries to take the strand a bisulfite read
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341 originated from into account
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342 (this is different from ordinary DNA alignment flags!)
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343 3 RNAME chromosome
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344 4 POS start position
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345 5 MAPQ always 255
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346 6 CIGAR extended CIGAR string
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347 7 MRNM Mate Reference sequence NaMe ('=' if same as RNAME)
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348 8 MPOS 1-based Mate POSition
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349 9 ISIZE Inferred insert SIZE
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350 10 SEQ query SEQuence on the same strand as the reference
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351 11 QUAL Phred33 scale
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352 12 NM-tag edit distance to the reference)
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353 13 XX-tag base-by-base mismatches to the reference.
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354 This does not include indels.
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355 14 XM-tag methylation call string
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356 15 XR-tag read conversion state for the alignment
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357 16 XG-tag genome conversion state for the alignment
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358
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359
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360 Each read of paired-end alignments is written out in a separate line in the above format.
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361
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362
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363 It looks like this (scroll sideways to see the entire example)::
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364
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365 QNAME FLAG RNAME POS MAPQ CIAGR MRNM MPOS ISIZE SEQ QUAL OPT
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366 HWI-EAS91_1_30788AAXX:1:1:1761:343 4 * 0 0 * * 0 0 AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
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367 HWI-EAS91_1_30788AAXX:1:1:1578:331 4 * 0 0 * * 0 0 GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
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368
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369 -------
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370
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371 **Bismark settings**
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372
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373 All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
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374
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375 ------
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376
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377 **Bismark parameter list**
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378
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379 This is an exhaustive list of Bismark options:
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380
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381 ------
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382
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383 **OPTIONS**
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384
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385
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386 Input::
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387
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388 --singles A comma- or space-separated list of files containing the reads to be aligned (e.g.
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389 lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
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390 produce one mapping result and one report file per input file.
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391
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392 -1 mates1 Comma-separated list of files containing the #1 mates (filename usually includes
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393 "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
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394 correspond file-for-file and read-for-read with those specified in mates2.
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395 Reads may be a mix of different lengths. Bismark will produce one mapping result
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396 and one report file per paired-end input file pair.
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397
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398 -2 mates2 Comma-separated list of files containing the #2 mates (filename usually includes
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399 "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
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400 correspond file-for-file and read-for-read with those specified in mates1.
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401 Reads may be a mix of different lengths.
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402
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403 -q/--fastq The query input files (specified as mate1,mate2 or singles are FASTQ
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404 files (usually having extension .fg or .fastq). This is the default. See also
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405 --solexa-quals.
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406
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407 -f/--fasta The query input files (specified as mate1,mate2 or singles are FASTA
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408 files (usually havin extension .fa, .mfa, .fna or similar). All quality values
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409 are assumed to be 40 on the Phred scale.
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410
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411 -s/--skip INT Skip (i.e. do not align) the first INT reads or read pairs from the input.
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412
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413 -u/--upto INT Only aligns the first INT reads or read pairs from the input. Default: no limit.
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414
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415 --phred33-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
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416
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417 --phred64-quals FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
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418
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419 --solexa-quals Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
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420 (which can't). The formula for conversion is:
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421 phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
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422 is usually the right option for use with (unconverted) reads emitted by the GA
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423 Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
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424
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425 --solexa1.3-quals Same as --phred64-quals. This is usually the right option for use with (unconverted)
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426 reads emitted by GA Pipeline version 1.3 or later. Default: off.
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427
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428
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429 Alignment::
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430
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431 -n/--seedmms INT The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
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432 of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the
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433 default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
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434
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435 -l/--seedlen The "seed length"; i.e., the number of bases of the high quality end of the read to
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436 which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
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437 larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
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438
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439 -e/--maqerr INT Maximum permitted total of quality values at all mismatched read positions throughout
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440 the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
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441 quality values to the nearest 10 and saturates at 30. This value is not relevant for
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442 Bowtie 2.
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443
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444 --chunkmbs INT The number of megabytes of memory a given thread is given to store path descriptors in
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445 --best mode. Best-first search must keep track of many paths at once to ensure it is
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446 always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
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447 memory impact of the descriptors, but they can still grow very large in some cases. If
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448 you receive an error message saying that chunk memory has been exhausted in --best mode,
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449 try adjusting this parameter up to dedicate more memory to the descriptors. This value
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450 is not relevant for Bowtie 2. Default: 512.
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451
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452 -I/--minins INT The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
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453 a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
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454 with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
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455 satisfied). A 19-bp gap would not be valid in that case. Default: 0.
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456
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457 -X/--maxins INT The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
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458 a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
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459 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
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460 A 61-bp gap would not be valid in that case. Default: 500.
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461
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462
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463
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464 Output::
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465
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466 --non_directional The sequencing library was constructed in a non strand-specific manner, alignments to all four
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467 bisulfite strands will be reported. Default: OFF.
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468
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469 (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
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470 to the original strands are merely theoretical and should not exist in reality. Specifying directional
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471 alignments (which is the default) will only run 2 alignment threads to the original top (OT)
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472 or bottom (OB) strands in parallel and report these alignments. This is the recommended option
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473 for sprand-specific libraries).
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474
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475 --sam-no-hd Suppress SAM header lines (starting with @). This might be useful when very large input files are
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476 split up into several smaller files to run concurrently and the output files are to be merged.
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477
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478 --quiet Print nothing besides alignments.
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479
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480 --vanilla Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
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481 of SAM format output.
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482
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483 -un/--unmapped Write all reads that could not be aligned to a file in the output directory. Written reads will
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484 appear as they did in the input, without any translation of quality values that may have
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485 taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
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486 and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
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487 with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
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488 are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
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489
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490 --ambiguous Write all reads which produce more than one valid alignment with the same number of lowest
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491 mismatches or other reads that fail to align uniquely to a file in the output directory.
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492 Written reads will appear as they did in the input, without any of the translation of quality
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493 values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
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494 parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
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495 _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
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496
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497 -o/--output_dir DIR Write all output files into this directory. By default the output files will be written into
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498 the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
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499 to create it first. The path to the output folder can be either relative or absolute.
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500
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501 --temp_dir DIR Write temporary files to this directory instead of into the same directory as the input files. If
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502 the specified folder does not exist, Bismark will attempt to create it first. The path to the
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503 temporary folder can be either relative or absolute.
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504
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505 ------
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506
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507 Bowtie 2 alignment options::
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508
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509 -N INT Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
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510 Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
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511 but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
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512 Bowtie 1 see -n).
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513
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514 -L INT Sets the length of the seed substrings to align during multiseed alignment. Smaller values
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515 make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
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516 used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
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517 Bowtie 1 see -l).
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518
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519 --ignore-quals When calculating a mismatch penalty, always consider the quality value at the mismatched
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520 position to be the highest possible, regardless of the actual value. I.e. input is treated
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521 as though all quality values are high. This is also the default behavior when the input
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522 doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
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523
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524
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525 Bowtie 2 paired-end options::
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526
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527 --no-mixed This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
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528 it cannot find a concordant or discordant alignment for a pair. This option is invariable and
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529 and on by default.
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530
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531 --no-discordant Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
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532 A discordant alignment is an alignment where both mates align uniquely, but that does not
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533 satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
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534 and it is on by default.
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535
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536
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537 Bowtie 2 effort options::
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538
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539 -D INT Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
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540 the alignments found so far. A seed extension "fails" if it does not yield a new best or a
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541 new second-best alignment. Default: 15.
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542
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543 -R INT INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
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544 When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
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545 mismatches allowed) at different offsets and searches for more alignments. A read is considered
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546 to have repetitive seeds if the total number of seed hits divided by the number of seeds
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547 that aligned at least once is greater than 300. Default: 2.
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548
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549
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550 Bowtie 2 Scoring options::
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551
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552 --score_min "func" Sets a function governing the minimum alignment score needed for an alignment to be considered
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553 "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
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554 L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
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555 See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
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556 L,0,-0.2.
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557
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558
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559 Bowtie 2 Reporting options::
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560
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561 --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
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562 deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
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563 default mode, but adjusting the -M setting is deprecated. Use the -D and -R options to adjust the
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564 effort expended to find valid alignments.
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565
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566 For reference, this used to be the old (now deprecated) description of -M:
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567 Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
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568 can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
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569 happens first. Only the best alignment is reported. Information from the other alignments is used to
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570 estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes
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571 Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
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572 aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
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573 guarantee that the alignment reported is the best possible in terms of alignment score. -M is
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574 always used and its default value is set to 10.
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575
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576 </help>
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577 </tool>
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