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Updated for cutadapt 0.9.4, no longer need python wrapper
author Lance Parsons <lparsons@princeton.edu>
date Wed, 25 May 2011 18:54:09 -0400
parents f6b94b76d16b
children 0a872e59164c
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3
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1 <tool id="cutadapt" name="Remove adapter sequences" version="0.9.4">
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2 <description>from high-throughput sequence data</description>
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3 <requirements>
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4 <requirement type="python-module">cutadapt</requirement>
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5 </requirements>
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6
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7 <command>cutadapt
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8 #if $input.extension.startswith( "fastq"):
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9 --format=fastq
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10 #else
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11 --format=$input.extension
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12 #end if
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13 #for $a in $adapters
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14 -a '${a.adapter_source.adapter}'
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15 #end for
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16 #for $aa in $anywhere_adapters
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17 -b '${aa.anywhere_adapter_source.anywhere_adapter}'
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18 #end for
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19 -e $error_rate
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20 -n $count
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21 -O $overlap
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22 #if str($min) != '0':
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23 -m $min
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24 #end if
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25 #if str($max) != '0':
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26 -M $max
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27 #end if
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28 #if $discard:
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29 --discard
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30 #end if
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31 '$input'
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32 --output='$output'
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33 2> $report
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34 </command>
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35 <inputs>
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36 <param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>
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37
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38 <repeat name="adapters" title="3' Adapters">
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39 <conditional name="adapter_source">
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40 <param name="adapter_source_list" type="select" label="Source" >
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41 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
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42 <option value="user">Enter custom sequence</option>
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43 </param>
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44
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45 <when value="user">
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46 <param name="adapter" size="30" label="Enter custom 3' adapter sequence" type="text" value="AATTGGCC" help="Sequence of an adapter that was ligated to the 3' end. The adapter itself and anything that follows is trimmed. If multiple adapters are specified, only the best matching adapter is trimmed."/>
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47 </when>
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48
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49 <when value="prebuilt">
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50 <param name="adapter" type="select" label="Choose 3' adapter" help="Sequence of an adapter that was ligated to the 3' end. The adapter itself and anything that follows is trimmed. If multiple adapters are specified, only the best matching adapter is trimmed.">
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51 <options from_file="fastx_clipper_sequences.txt">
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52 <column name="name" index="1"/>
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53 <column name="value" index="0"/>
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54 </options>
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55 </param>
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56 </when>
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57 </conditional>
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58 </repeat>
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59
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60 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that was ligated to the 5' or 3' end. If the adapter is found within the read or overlapping the 3' end of the read, the behavior is the same as for the -a option. If the adapter overlaps the 5' end (beginning of the read), the initial portion of the read matching the adapter is trimmed, but anything that follows is kept. If multiple -a or -b options are given, only the best matching adapter is trimmed.">
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61 <conditional name="anywhere_adapter_source">
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62 <param name="anywhere_adapter_source_list" type="select" label="Source">
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63 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
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64 <option value="user">Enter custom sequence</option>
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65 </param>
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66
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67 <when value="user">
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68 <param name="anywhere_adapter" size="30" label="Enter custom 5' or 3' adapter sequence" type="text" value="AATTGGCC" help="Sequence of an adapter that was ligated to the 5' or 3' end. If the adapter is found within the read or overlapping the 3' end of the read, the behavior is the same as for the -a option. If the adapter overlaps the 5' end (beginning of the read), the initial portion of the read matching the adapter is trimmed, but anything that follows is kept. If multiple -a or -b options are given, only the best matching adapter is trimmed."/>
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69 </when>
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70 <when value="prebuilt">
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71 <param name="anywhere_adapter" type="select" label="Choose 5' or 3' adapter" help="Sequence of an adapter that was ligated to the 5' or 3' end. If the adapter is found within the read or overlapping the 3' end of the read, the behavior is the same as for the -a option. If the adapter overlaps the 5' end (beginning of the read), the initial portion of the read matching the adapter is trimmed, but anything that follows is kept. If multiple -a or -b options are given, only the best matching adapter is trimmed.">
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72 <options from_file="fastx_clipper_sequences.txt">
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73 <column name="name" index="1"/>
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74 <column name="value" index="0"/>
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75 </options>
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76 </param>
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77 </when>
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78 </conditional>
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79 </repeat>
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80
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81 <param name="error_rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
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82 <param name="count" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
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83 <param name="overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified." />
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84 <param name="discard" type="boolean" checked="False" default="False" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
0
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85 <param name="min" type="integer" min="0" optional="true" value="0" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no minimum length." />
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86 <param name="max" type="integer" min="0" optional="true" value="0" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no maximum length." />
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87 </inputs>
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88 <outputs>
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89 <data format="txt" name="report" label="${tool.name} on ${on_string} (Report)" />
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90 <data format="input" name="output" metadata_source="input"/>
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91 </outputs>
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92
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93 <tests>
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94 <test>
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95 <param name="input" value="fa_gc_content_input.fa"/>
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96 <output name="out_file1" file="fa_gc_content_output.txt"/>
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97 </test>
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98 </tests>
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99
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100 <help>
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101 This tool removes adapter sequences from DNA high-throughput
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102 sequencing data. This is usually necessary when the read length of the
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103 machine is longer than the molecule that is sequenced, such as in
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104 microRNA data.
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105
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106 The tool is based on the opensource cutadapt_ tool.
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107
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108 -----
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109
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110 **Algorithm**
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111
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112 cutadapt uses a simple semi-global alignment algorithm, without any special optimizations.
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113 For speed, the algorithm is implemented as a Python extension module in calignmodule.c.
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114
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115
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116 **Partial adapter matches**
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117
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118 Cutadapt correctly deals with partial adapter matches. As an example, suppose
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119 your adapter sequence is "ADAPTER" (specified via 3' Adapters parameter).
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120 If you have these input sequences:
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121
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122 ::
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123
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124 MYSEQUENCEADAPTER
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125 MYSEQUENCEADAP
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126 MYSEQUENCEADAPTERSOMETHINGELSE
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127
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128 All of them will be trimmed to "MYSEQUENCE". If the sequence starts with an
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129 adapter, like this:
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130
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131 ::
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132
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133 ADAPTERSOMETHING
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134
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135 It will be empty after trimming.
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136
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137 When the allowed error rate is sufficiently high, errors in
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138 the adapter sequence are allowed. For example, ADABTER (1 mismatch), ADAPTR (1 deletion),
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139 and ADAPPTER (1 insertion) will all be recognized if the error rate is set to 0.15.
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140
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141
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142 **Allowing adapters anywhere**
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143
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144 Cutadapt assumes that any adapter specified via the *3` Adapters* parameter
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145 was ligated to the 3' end of the sequence. This is the correct assumption for
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146 at least the SOLiD and Illumina small RNA protocols and probably others.
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147
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148 If, on the other hand, your adapter can also be ligated to the 5' end (on
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149 purpose or by accident), you should tell cutadapt so by using the *5' or 3' (Anywhere)
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150 Adapters* parameter. It will then use a different alignment algorithm and
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151 correctly trim adapters that appear in the beginning of a read. An adapter
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152 specified this way will also be found if it appears only partially in the
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153 beginning of a read. For example, these sequences
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154
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155 ::
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156
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157 ADAPTERMYSEQUENCE
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158 PTERMYSEQUENCE
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159
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160 will be trimmed to "MYSEQUENCE". Note that the regular algorithm would trim
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161 the first read to an empty sequence.
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162
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163 This parameter currently does not work with color space data.
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164
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165
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166 .. _cutadapt: http://code.google.com/p/cutadapt/
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167 </help>
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168
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169 </tool>