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annotate cutadapt.xml @ 2:f6b94b76d16b

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author Lance Parsons <lparsons@princeton.edu>
date Mon, 16 May 2011 16:34:09 -0400
parents 8b064ea16722
children 7ed26fc9fa8a
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1 <tool id="cutadapt" name="Remove adapter sequences" version="0.9.3">
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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 interpreter="python">cutadapt_galaxy_wrapper.py
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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 $max
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27 #end if
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28 --input='$input'
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29 --output='$output'
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30 > $report
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31 </command>
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32 <inputs>
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33 <param format="fastqsanger, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>
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34
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35 <repeat name="adapters" title="3' Adapters">
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36 <conditional name="adapter_source">
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37 <param name="adapter_source_list" type="select" label="Source" >
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38 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
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39 <option value="user">Enter custom sequence</option>
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40 </param>
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41
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42 <when value="user">
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43 <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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44 </when>
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45
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46 <when value="prebuilt">
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47 <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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48 <options from_file="fastx_clipper_sequences.txt">
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49 <column name="name" index="1"/>
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50 <column name="value" index="0"/>
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51 </options>
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52 </param>
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53 </when>
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54 </conditional>
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55 </repeat>
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56
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57 <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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58 <conditional name="anywhere_adapter_source">
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59 <param name="anywhere_adapter_source_list" type="select" label="Source">
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60 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
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61 <option value="user">Enter custom sequence</option>
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62 </param>
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63
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64 <when value="user">
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65 <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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66 </when>
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67 <when value="prebuilt">
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68 <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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69 <options from_file="fastx_clipper_sequences.txt">
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70 <column name="name" index="1"/>
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71 <column name="value" index="0"/>
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72 </options>
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73 </param>
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74 </when>
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75 </conditional>
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76 </repeat>
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77
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78 <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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79 <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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80 <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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81 <!--<param name="discard" type="boolean" checked="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!" />-->
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82 <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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83 <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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84 </inputs>
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85 <outputs>
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86 <data format="txt" name="report" label="${tool.name} on ${on_string} (Report)" />
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87 <data format="input" name="output" metadata_source="input"/>
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88 </outputs>
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89
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90 <tests>
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91 <test>
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92 <param name="input" value="fa_gc_content_input.fa"/>
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93 <output name="out_file1" file="fa_gc_content_output.txt"/>
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94 </test>
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95 </tests>
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96
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97 <help>
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98 This tool removes adapter sequences from DNA high-throughput
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99 sequencing data. This is usually necessary when the read length of the
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100 machine is longer than the molecule that is sequenced, such as in
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101 microRNA data.
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102
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103 The tool is based on the opensource cutadapt_ tool.
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104
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105 -----
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106
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107 **Algorithm**
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108
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109 cutadapt uses a simple semi-global alignment algorithm, without any special optimizations.
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110 For speed, the algorithm is implemented as a Python extension module in calignmodule.c.
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111
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112
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113 **Partial adapter matches**
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114
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115 Cutadapt correctly deals with partial adapter matches. As an example, suppose
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116 your adapter sequence is "ADAPTER" (specified via 3' Adapters parameter).
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117 If you have these input sequences:
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118
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119 ::
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120
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121 MYSEQUENCEADAPTER
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122 MYSEQUENCEADAP
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123 MYSEQUENCEADAPTERSOMETHINGELSE
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124
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125 All of them will be trimmed to "MYSEQUENCE". If the sequence starts with an
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126 adapter, like this:
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127
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128 ::
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129
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130 ADAPTERSOMETHING
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131
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132 It will be empty after trimming.
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133
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134 When the allowed error rate is sufficiently high, errors in
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135 the adapter sequence are allowed. For example, ADABTER (1 mismatch), ADAPTR (1 deletion),
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136 and ADAPPTER (1 insertion) will all be recognized if the error rate is set to 0.15.
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137
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138
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139 **Allowing adapters anywhere**
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140
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141 Cutadapt assumes that any adapter specified via the *3` Adapters* parameter
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142 was ligated to the 3' end of the sequence. This is the correct assumption for
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143 at least the SOLiD and Illumina small RNA protocols and probably others.
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144
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145 If, on the other hand, your adapter can also be ligated to the 5' end (on
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146 purpose or by accident), you should tell cutadapt so by using the *5' or 3' (Anywhere)
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147 Adapters* parameter. It will then use a different alignment algorithm and
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148 correctly trim adapters that appear in the beginning of a read. An adapter
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149 specified this way will also be found if it appears only partially in the
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150 beginning of a read. For example, these sequences
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151
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152 ::
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153
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154 ADAPTERMYSEQUENCE
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155 PTERMYSEQUENCE
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156
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157 will be trimmed to "MYSEQUENCE". Note that the regular algorithm would trim
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158 the first read to an empty sequence.
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159
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160 This parameter currently does not work with color space data.
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161
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162
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163 .. _cutadapt: http://code.google.com/p/cutadapt/
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164 </help>
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165
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166 </tool>