annotate cutadapt.xml @ 19:49370cb85f0f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
author iuc
date Tue, 18 Dec 2018 14:09:53 -0500
parents 5c7e7d905b33
children e4691e1589d3
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49370cb85f0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
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1 <tool id="cutadapt" name="Cutadapt" version="1.16.5" profile="17.09">
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2 <description>Remove adapter sequences from Fastq/Fasta</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.16">cutadapt</requirement>
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8 </requirements>
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9
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2d6671b10919 Updated to support cutadapt version 1.1 (also include automatic dependency installation)
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10 <version_command>cutadapt --version</version_command>
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
parents:
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11
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12 <command detect_errors="exit_code"><![CDATA[
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13 ## Link in the input and output files, so Cutadapt can tell their type
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14
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15 #import re
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16 #set read1 = "input_f"
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17 #set read2 = "input_r"
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18 #set paired = False
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19 #set library_type = str($library.type)
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20 #if $library_type == 'paired':
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21 #set paired = True
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22 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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23 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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24 #set input_1 = $library.input_1
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25 #set input_2 = $library.input_2
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26 #else if $library_type == 'paired_collection'
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27 #set paired = True
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28 #set input_1 = $library.input_1.forward
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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29 #set input_2 = $library.input_1.reverse
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30 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1"
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31 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_2"
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32 #else
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33 #set input_1 = $library.input_1
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34 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
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35 #end if
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36
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37 #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
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38 #set read1 = $read1 + ".fq.gz"
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39 #set out1 = "out1.gz"
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40 #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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41 #set read1 = $read1 + ".fq.bz2"
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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42 #set out1 = "out1.bz2"
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43 #else if $input_1.is_of_type('fasta'):
f5fdf41c08b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 1663496ce146a311569a340b0b809dc5127e0830
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44 #set read1 = $read1 + ".fa"
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45 #set out1 = "out1.fa"
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46 #else:
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47 #set read1 = $read1 + ".fq"
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48 #set out1 = "out1.fq"
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49 #end if
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50 ln -f -s '${input_1}' '$read1' &&
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51
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52 #if $paired:
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53 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
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54 #set read2 = $read2 + ".fq.gz"
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55 #set out2 = "out2.gz"
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56 #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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57 #set read2 = $read2 + ".fq.bz2"
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58 #set out2 = "out2.bz2"
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59 #else if $input_2.is_of_type('fasta'):
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60 #set read2 = $read2 + ".fa"
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61 #set out2 = "out2.fa"
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62 #else:
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63 #set read2 = $read2 + ".fq"
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64 #set out2 = "out2.fq"
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65 #end if
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66 ln -f -s '${input_2}' '$read2' &&
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67 #end if
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68
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69 ## Run Cutadapt
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70
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71 #if $output_options.multiple_output:
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72 mkdir split &&
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73 #end if
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74
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75 cutadapt
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76
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77 ## cutadapt (up to version 1.16) can't be run in multicore mode with these options
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78 #if not any(($output_options.info_file, $output_options.rest_file, $output_options.wildcard_file, $output_options.too_short_file, $output_options.too_long_file, $output_options.untrimmed_file))
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79 -j \${GALAXY_SLOTS:-1}
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80 #end if
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81
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82 #if str( $library.type ) == "single":
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83 @read1_options@
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84 #if $output_options.multiple_output:
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85 --output='split/{name}.${input_1.ext}'
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86 #else:
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87 --output='$out1'
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88 #end if
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89 #else:
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90 @read1_options@
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91 @read2_options@
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92 --output='$out1'
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93 --paired-output='$out2'
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94 #end if
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95
13
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96 --error-rate=$adapter_options.error_rate
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97 --times=$adapter_options.count
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98 --overlap=$adapter_options.overlap
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99 $adapter_options.no_indels
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100 $adapter_options.match_read_wildcards
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101 $adapter_options.no_trim
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102 $adapter_options.mask_adapter
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103
13
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104 $filter_options.discard
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105 $filter_options.discard_untrimmed
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106 #if str($filter_options.min) != '0':
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107 --minimum-length=$filter_options.min
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108 #end if
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109 #if str($filter_options.max) != '0':
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110 --maximum-length=$filter_options.max
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111 #end if
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112 #if $filter_options.max_n:
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113 --max-n=$filter_options.max_n
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114 #end if
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115 #if str( $library.type ) != "single":
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116 #if $filter_options.pair_filter:
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117 --pair-filter=$filter_options.pair_filter
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118 #end if
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119 #end if
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120
93d58ffe39f1 Updated to version 1.6
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121
13
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122 #if str($read_mod_options.quality_cutoff) != '0':
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123 --quality-cutoff=$read_mod_options.quality_cutoff
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124 #end if
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125 #if str($read_mod_options.nextseq_trim) != '0':
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126 --nextseq-trim=$read_mod_options.nextseq_trim
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127 #end if
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128 $read_mod_options.trim_n
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129 #if $read_mod_options.prefix != '':
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130 --prefix="$read_mod_options.prefix"
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131 #end if
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132 #if $read_mod_options.suffix != '':
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133 --suffix="$read_mod_options.suffix"
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134 #end if
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135 #if str($read_mod_options.length) != '0':
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136 --length=$read_mod_options.length
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137 #end if
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138 #if $read_mod_options.length_tag != '':
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139 --length-tag="$read_mod_options.length_tag"
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140 #end if
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141
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142 '${read1}'
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143 #if $paired:
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144 '${read2}'
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145 #end if
0
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146
13
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147 #if $output_options.report:
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148 > report.txt
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149 #end if
11
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150 ]]></command>
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151 <inputs>
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152
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153 <!-- Reads -->
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154 <conditional name="library">
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155 <param name="type" type="select" label="Single-end or Paired-end reads?">
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156 <option value="single">Single-end</option>
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157 <option value="paired">Paired-end</option>
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158 <option value="paired_collection">Paired-end Collection</option>
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159 </param>
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160
11
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161 <when value="single">
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162 <param name="input_1" format="fastq.gz,fastq,fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTQ/A file" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
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163 <expand macro="single_end_options" />
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164 </when>
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165
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166 <when value="paired">
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167 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTQ/A file #1" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
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168 <param name="input_2" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data" label="FASTQ/A file #2" help="Should be of datatype &quot;fastq.gz&quot;or &quot;fasta&quot;" />
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169 <expand macro="paired_end_options" />
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170 </when>
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171
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172 <when value="paired_collection">
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173 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
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174 <expand macro="paired_end_options" />
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175 </when>
12
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176
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177 </conditional>
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178
11
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179 <!-- Adapter Options -->
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180 <section name="adapter_options" title="Adapter Options">
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181 <param name="error_rate" argument="--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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182 <param name="no_indels" argument="--no-indels" type="boolean" value="False" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
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183 <param name="count" argument="--times" 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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184 <param name="overlap" argument="--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. This reduces the number of bases trimmed purely due to short random adapter matches." />
16
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185 <param name="match_read_wildcards" type="select" label="Match Wildcards" help="Allow 'N's as matches. Default: In the adapters but not in the reads">
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186 <option value=" " selected="True">In the adapters but not in the reads</option>
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187 <option value="--match-read-wildcards">In the adapters and in the reads</option>
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188 <option value="--no-match-adapter-wildcards">Nowhere</option>
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189 </param>
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190 <param name="no_trim" argument="--no-trim" type="boolean" value="False" truevalue="--no-trim" falsevalue="" label="Do not trim adapters" help="Match and redirect reads to output/untrimmed-output as usual, but don't remove the adapters (default: trim the adapters)." />
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191 <param name="mask_adapter" argument="--mask-adapter" type="boolean" value="False" truevalue="--mask-adapter" falsevalue="" label="Mask Adapters" help="Mask adapter bases with 'N' instead of trimming them (default: trim adapters)." />
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192 </section>
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193
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194 <!-- Filter Options -->
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195 <section name="filter_options" title="Filter Options">
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196 <param name="discard" argument="--discard-trimmed" type="boolean" value="False" truevalue="--discard" falsevalue="" 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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197 <param name="discard_untrimmed" argument="--discard_untrimmed" type="boolean" value="False" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
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198 <param name="min" argument="--minimum-length" 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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199 <param name="max" argument="--maximum-length" 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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200 <param name="max_n" argument="--max-n" type="float" min="0" optional="True" label="Max N" help="Discard reads with more than this number of 'N' bases. A number between 0 and 1 is interpreted as a fraction of the read length." />
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201 <param name="pair_filter" argument="--pair-filter" type="select" optional="True" label="Pair filter" help="Which of the reads in a paired-end read have to match the filtering criterion in order for the pair to be filtered. Default: any">
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202 <option value="any" selected="True">any</option>
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203 <option value="both">both</option>
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204 </param>
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205 </section>
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206
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207 <!-- Read Modification Options -->
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208 <section name="read_mod_options" title="Read Modification Options">
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209 <param name="quality_cutoff" argument="--quality-cutoff" type="text" value="0" label="Quality cutoff" help=" Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. Applied to both reads if data is paired. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second.">
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210 <sanitizer>
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211 <valid initial="string.digits"><add value="," /></valid>
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212 </sanitizer>
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213 </param>
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214 <param name="nextseq_trim" argument="--nextseq-trim" type="integer" value="0" label="NextSeq trimming" help="Experimental option for quality trimming of NextSeq data. This is necessary because that machine cannot distinguish between G and reaching the end of the fragment (it encodes G as ‘black’). This option works like regular quality trimming (where one would use -q 20 instead), except that the qualities of G bases are ignored." />
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215 <param name="trim_n" argument="--trim-n" type="boolean" truevalue="--trim-n" falsevalue="" checked="False" label="Trim Ns" help="Trim N's on ends of reads." />
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216 <param name="prefix" argument="--prefix" label="Prefix" type="text" help="Add this prefix to read names" />
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217 <param name="suffix" argument="--suffix" label="Suffix" type="text" help="Add this suffix to read names" />
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218 <param name="strip_suffix" argument="--strip-suffix" label="Strip suffix" type="text" help="Remove this suffix from read names if present." />
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219 <param name="length" argument="--length" type="integer" value="0" label="Length" help="Shorten reads to this length. This modification is applied after adapter trimming." />
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220 <param name="length_tag" argument="--length-tag" label="Length Tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." />
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221 </section>
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222
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223 <!-- Output Options -->
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224 <section name="output_options" title="Output Options">
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225 <param name="report" type="boolean" value="False" label="Report" help="Cutadapt's per-adapter statistics. You can use this file with MultiQC."/>
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226 <param name="info_file" argument="--info-file" type="boolean" value="False" label="Info File" help="Write information about each read and its adapter matches to a file."/>
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227 <param name="rest_file" argument="--rest-file" type="boolean" value="False" label="Rest of Read" help="When the adapter matches in the middle of a read, write the rest (after the adapter) into a file."/>
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228 <param name="wildcard_file" argument="--wildcard-file" type="boolean" value="False" label="Wildcard File" help="When the adapter has wildcard bases ('N's) write adapter bases matching wildcard positions to file."/>
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229 <param name="too_short_file" argument="--too-short-output" type="boolean" value="False" label="Too Short Reads" help="Write reads that are too short (according to minimum length specified) to a file. (default: discard reads)"/>
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230 <param name="too_long_file" argument="--too-long-output" type="boolean" value="False" label="Too Long Reads" help="Write reads that are too long (according to maximum length specified) to a file. (default: discard reads)"/>
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231 <param name="untrimmed_file" argument="--untrimmed-output" type="boolean" value="False" label="Untrimmed Reads" help="Write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file. (default: output to same file as trimmed)"/>
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232 <param name="multiple_output" argument="" type="boolean" value="False" label="Multiple output" help="Create a separate file for each adapter trimmed (default: all trimmed reads are in a single file)"/>
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233 </section>
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234
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235 </inputs>
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236
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237 <outputs>
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238 <data name="out1" format="fastqsanger" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
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239 <filter>(output_options['multiple_output'] is False)</filter>
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240 <expand macro="inherit_format_1" />
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241 </data>
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242 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >
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243 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
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244 <expand macro="inherit_format_2" />
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245 </data>
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246
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247 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
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248 <filter>(output_options['report'] is True)</filter>
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249 </data>
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250
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251 <data name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" >
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252 <filter>(output_options['info_file'] is True)</filter>
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253 </data>
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254
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255 <data name="rest_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
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256 <filter>(output_options['rest_file'] is True)</filter>
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257 <expand macro="inherit_format_1" />
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258 </data>
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259
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260 <data name="wild_output" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Wildcard File" >
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261 <filter>(output_options['wildcard_file'] is True)</filter>
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262 </data>
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263
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264 <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
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265 <filter>(output_options['untrimmed_file'] is True)</filter>
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266 <expand macro="inherit_format_1" />
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267 </data>
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268 <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
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269 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
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270 <filter>(output_options['untrimmed_file'] is True)</filter>
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271 <expand macro="inherit_format_2" />
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272 </data>
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273
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274 <data name="too_short_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Short Read 1" >
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275 <filter>(output_options['too_short_file'] is True)</filter>
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276 <expand macro="inherit_format_1" />
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277 </data>
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278 <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Short Read 2" >
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279 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
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280 <filter>(output_options['too_short_file'] is True)</filter>
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281 <expand macro="inherit_format_2" />
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282 </data>
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283
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284 <data name="too_long_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Long Read 1" >
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285 <filter>(output_options['too_long_file'] is True)</filter>
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286 <expand macro="inherit_format_1" />
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287 </data>
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288 <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Long Read 2" >
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289 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
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290 <filter>(output_options['too_long_file'] is True)</filter>
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291 <expand macro="inherit_format_2" />
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292 </data>
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293
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294 <collection name="split_output" type="list" label="${tool.name} on ${on_string}: Split outputs" >
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295 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;fastq.*)" directory="split" />
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296 <filter>(output_options['multiple_output'] is True)</filter>
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297 </collection>
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298
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299 </outputs>
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300
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301 <tests>
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302 <!-- Ensure fastq works -->
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303 <test>
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304 <param name="type" value="single" />
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305 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
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306 <param name="adapter_source_list" value="user"/>
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307 <param name="adapter" value="AGATCGGAAGAGC"/>
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308 <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
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309 </test>
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310 <!-- Ensure single end fastq.gz works -->
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311 <test>
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312 <param name="type" value="single" />
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313 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
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314 <param name="adapter_source_list" value="user"/>
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315 <param name="adapter" value="AGATCGGAAGAGC"/>
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316 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
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317 </test>
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318 <!-- Ensure paired end fastq.gz works -->
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319 <test>
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320 <param name="type" value="paired" />
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321 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
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322 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
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323 <param name="adapter_source_list" value="user"/>
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324 <param name="adapter" value="AGATCGGAAGAGC"/>
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325 <param name="adapter_source_list2" value="user"/>
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326 <param name="adapter2" value="AGATCGGAAGAGC"/>
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327 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
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328 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
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329 </test>
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330 <!-- Ensure paired collection works -->
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331 <test>
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332 <param name="type" value="paired_collection" />
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333 <param name="input_1">
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334 <collection type="paired">
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335 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
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336 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
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337 </collection>
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338 </param>
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339 <param name="adapter_source_list" value="user"/>
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340 <param name="adapter" value="AGATCGGAAGAGC"/>
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341 <param name="adapter_source_list2" value="user"/>
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342 <param name="adapter2" value="AGATCGGAAGAGC"/>
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343 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
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344 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
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345 </test>
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346 <!-- Ensure built-in adapters work -->
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347 <test>
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348 <param name="type" value="single" />
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349 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
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350 <param name="adapter_source_list" value="builtin"/>
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351 <param name="adapter" value="TGTAGGCC"/>
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352 <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
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353 </test>
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354 <!-- Ensure discard file output works -->
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355 <test>
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356 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
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357 <param name="adapter_source_list" value="user"/>
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358 <param name="adapter" value="TTAGACATATCTCCGTCG"/>
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359 <param name="output_filtering" value="filter"/>
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360 <param name="discard" value="True"/>
9
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lparsons
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361 <param name="read_modification" value="none"/>
93d58ffe39f1 Updated to version 1.6
lparsons
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362 <param name="output_type" value="default"/>
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363 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
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364 </test>
11
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365 <!-- Ensure rest file output works -->
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lparsons
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366 <test>
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367 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
9
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368 <param name="adapter_source_list" value="user"/>
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369 <param name="adapter" value="AAAGATG"/>
9
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370 <param name="output_filtering" value="default"/>
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371 <param name="read_modification" value="none"/>
93d58ffe39f1 Updated to version 1.6
lparsons
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372 <param name="output_type" value="additional"/>
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373 <param name="rest_file" value="True"/>
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374 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
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375 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
9
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lparsons
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376 </test>
11
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377 <!-- Ensure nextseq-trim option works -->
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iuc
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378 <test>
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iuc
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379 <param name="type" value="single" />
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iuc
parents: 10
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380 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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381 <param name="adapter_source_list" value="user"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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382 <param name="adapter" value="AGATCGGAAGAGC"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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383 <param name="read_modification" value="modify"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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384 <param name="nextseq_trim" value="20" />
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385 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
11
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386 </test>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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387 <!-- Ensure Report and Info file output work -->
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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388 <test>
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iuc
parents: 10
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389 <param name="type" value="single" />
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iuc
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390 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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391 <param name="adapter_source_list" value="user"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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392 <param name="adapter" value="AGATCGGAAGAGC"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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393 <param name="report" value="True" />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
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394 <param name="info_file" value="True" />
12
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iuc
parents: 11
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395 <output name="out1" value="cutadapt_small.out" ftype="fastq"/>
11
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iuc
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396 <output name="report">
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iuc
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397 <assert_contents>
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iuc
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398 <has_text text="Summary"/>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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399 </assert_contents>
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
iuc
parents: 10
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400 </output>
12
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401 <output name="info_file" value="cutadapt_info_out.txt" ftype="txt"/>
11
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402 </test>
16
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iuc
parents: 15
diff changeset
403
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
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404
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
405 <test>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
406 <conditional name="library">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
407 <param name="type" value="single" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
408 <param name="input_1" ftype="fastq" value="cutadapt_in_split.fastq" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
409 <section name="r1" >
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
410 <repeat name="front_adapters">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
411 <conditional name="front_adapter_source">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
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412 <param name="front_adapter_source_list" value="user"/>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
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413 <param name="front_adapter_name" value="A1" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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414 <param name="front_adapter" value="^GTCGGTAA" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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415 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
416 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
417 <repeat name="front_adapters">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
418 <conditional name="front_adapter_source">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
419 <param name="front_adapter_source_list" value="user"/>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
420 <param name="front_adapter_name" value="A2" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
421 <param name="front_adapter" value="^AGGTCACT" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
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422 </conditional>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
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423 </repeat>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
424 </section>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
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425 </conditional>
18
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diff changeset
426 <param name="report" value="False" />
16
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427 <param name="info_file" value="False" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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428 <param name="multiple_output" value="True" />
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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429 <output_collection name="split_output" type="list" count="3">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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diff changeset
430 <element name="A1" value="A1.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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diff changeset
431 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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diff changeset
432 <element name="A2" value="A2.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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diff changeset
433 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
434 <element name="unknown" value="unknown.fastq" ftype="fastq">
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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diff changeset
435 </element>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
436 </output_collection>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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diff changeset
437 </test>
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
parents: 15
diff changeset
438
8f1df515eb87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 034c93600ce3279644d05f3675b4820ef7180851
iuc
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439
18
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parents: 17
diff changeset
440 <test>
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
441 <conditional name="library">
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
442 <param name="type" value="single" />
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
443 <param name="input_1" ftype="fastq.gz" value="cutadapt_in_split.fastq.gz" />
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
444 <section name="r1" >
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
parents: 17
diff changeset
445 <repeat name="front_adapters">
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
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diff changeset
446 <conditional name="front_adapter_source">
19
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parents: 18
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447 <param name="front_adapter_source_list" value="file"/>
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iuc
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448 <param name="front_adapter_file" ftype="fasta" value="barcodes.fasta" />
18
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449 </conditional>
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
iuc
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diff changeset
450 </repeat>
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diff changeset
451 </section>
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
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diff changeset
452 </conditional>
5c7e7d905b33 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b58d6ff959a1d920fd0d9b02e43d2482667d61e8
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453 <param name="report" value="False" />
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454 <param name="info_file" value="False" />
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455 <param name="multiple_output" value="True" />
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456 <output_collection name="split_output" type="list" count="3">
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457 <element name="A1" decompress="True" file="A1.fastq.gz" ftype="fastq.gz">
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458 </element>
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459 <element name="A2" decompress="True" file="A2.fastq.gz" ftype="fastq.gz">
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460 </element>
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461 <element name="unknown" decompress="True" file="unknown.fastq.gz" ftype="fastq.gz">
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462 </element>
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463 </output_collection>
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464 </test>
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465
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466 </tests>
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467
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468 <help><![CDATA[
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469
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470 .. class:: infomark
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471
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472 **What it does**
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473
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474 -------------------
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475
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476 **Cutadapt** finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
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477
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478 Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced, such as in microRNA, or CRISPR data, or Poly-A tails that are useful for pulling out RNA from your sample but often you don’t want them to be in your reads.
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479
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480 Cutadapt_ helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter reads in various ways. Cutadapt searches for the adapter in all reads and removes it when it finds it. Unless you use a filtering option, all reads that were present in the input file will also be present in the output file, some of them trimmed, some of them not. Even reads that were trimmed entirely (because the adapter was found in the very beginning) are output. All of this can be changed with options in the tool form above.
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481
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482 The tool is based on the **Open Source** Cutadapt_ tool. See the complete `Cutadapt documentation`_ for additional details. If you use Cutadapt, please cite *Marcel, 2011* under **Citations** below.
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483
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484 -------------------
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485
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486 **Inputs**
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487
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488 -------------------
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489
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490 Input files for Cutadapt need to be:
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491
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492 - FASTQ.GZ, FASTQ.BZ2, FASTQ or FASTA
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493
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494 To trim an adapter, input the ADAPTER sequence in plain text or in a FASTA file e.g. AACCGGTT (with the characters: **$**, **^**, **...**, if anchored or linked).
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495
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496 ============================================= ===================
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497 **Option** **Sequence**
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498 --------------------------------------------- -------------------
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499 3’ (End) Adapter ADAPTER
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500 Anchored 3’ Adapter ADAPTER$
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501
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502 5’ (Front) Adapter ADAPTER
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503 Anchored 5’ Adapter ^ADAPTER
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504
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505 5’ or 3’ (Both possible) ADAPTER
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506
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507 Linked Adapter - 3' (End) only ADAPTER1...ADAPTER2
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508 Non-anchored Linked Adapter - 5' (Front) only ADAPTER1...ADAPTER2
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509 ============================================= ===================
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510
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511 Below is an illustration of the allowed adapter locations relative to the read and depending on the adapter type:
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512
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513 .. image:: $PATH_TO_IMAGES/adapters.svg
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514
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515
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516 -------------------
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517
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518 *Example: Illumina TruSeq Adapters*
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519
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520 -------------------
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521
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522 If you have reads containing Illumina TruSeq adapters, for example, follow these steps.
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523
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524
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525 For Single-end reads as well as the first reads of Paired-end data:
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526
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527 **Read 1**
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528
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529 In the **3' (End) Adapters** option above, insert A + the “TruSeq Indexed Adapter” prefix that is common to all Indexed Adapter sequences, e.g insert:
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530
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531 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
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532
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533
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534 For the second reads of Paired-end data:
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535
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536 **Read 2**
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537
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538 In the **3' (End) Adapters** option above, insert the reverse complement of the “TruSeq Universal Adapter”:
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539
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540 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
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541
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542 The adapter sequences can be found in the document `Illumina TruSeq Adapters De-Mystified`_.
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543
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544 -----------
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545
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546 **Outputs**
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547
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548 -----------
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549
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550 - Trimmed reads
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551
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552 Optionally, under **Output Options** you can choose to output
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553
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554 * Report
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555 * Info file
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556
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557
11
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558 **Report**
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559
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560 Cutadapt can output per-adapter statistics if you select to output the report above.
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561
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562 Example:
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563
11
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564 *This is cutadapt 1.16 with Python 3.6.4*
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565
11
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566 *Command line parameters: -j 1 --format=fastq -a AGATCGGAAGAGC --info-file=/tmp/tmpX0DlY1/files/000/dataset_21.dat --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 input_f.fastq*
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567 *Running on 1 core*
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568 *Trimming 1 adapter with at most 10.0% errors in single-end mode ...*
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569 *Finished in 0.00 s (1426 us/read; 0.04 M reads/minute).*
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570
11
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571 *=== Summary ===*
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572
11
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573 * Total reads processed: 3*
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574 * Reads with adapters: 0 (0.0%)*
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575 * Reads written (passing filters): 3 (100.0%)*
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576
11
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577 * Total basepairs processed: 102 bp*
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578 * Total written (filtered): 102 bp (100.0%)*
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579
11
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580 *=== Adapter 1 ===*
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581
11
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582 *Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times.*
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583
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584
11
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585 **Info file**
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586
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587 The info file contains information about the found adapters. The output is a tab-separated text file. Each line corresponds to one read of the input file.
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588
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589 Columns contain the following data:
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590
11
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591 * **1st**: Read name
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592 * **2nd**: Number of errors
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593 * **3rd**: 0-based start coordinate of the adapter match
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594 * **4th**: 0-based end coordinate of the adapter match
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595 * **5th**: Sequence of the read to the left of the adapter match (can be empty)
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596 * **6th**: Sequence of the read that was matched to the adapter
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597 * **7th**: Sequence of the read to the right of the adapter match (can be empty)
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598 * **8th**: Name of the found adapter
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599 * **9th**: Quality values corresponding to sequence left of the adapter match (can be empty)
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600 * **10th**: Quality values corresponding to sequence matched to the adapter (can be empty)
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601 * **11th**: Quality values corresponding to sequence to the right of the adapter (can be empty)
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602
11
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603 The concatenation of columns 5-7 yields the full read sequence. Column 8 identifies the found adapter. Adapters without a name are numbered starting from 1. Fields 9-11 are empty if quality values are not available. Concatenating them yields the full sequence of quality values.
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604
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605 If no adapter was found, the format is as follows:
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606
11
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607 #. Read name
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608 #. The value -1
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609 #. The read sequence
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610 #. Quality values
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611
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612 When parsing the file, be aware that additional columns may be added in the future. Note also that some fields can be empty, resulting in consecutive tabs within a line.
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613
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614 If the --times option is used and greater than 1, each read can appear more than once in the info file. There will be one line for each found adapter, all with identical read names. Only for the first of those lines will the concatenation of columns 5-7 be identical to the original read sequence (and accordingly for columns 9-11). For subsequent lines, the shown sequence are the ones that were used in subsequent rounds of adapter trimming, that is, they get successively shorter.
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615
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616 --------------------
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617
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618 **More Information**
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619
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620 --------------------
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621
11
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622 See the excellent `Cutadapt documentation`_
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623
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624 .. _Cutadapt: https://cutadapt.readthedocs.io/en/stable/
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625 .. _`Cutadapt documentation`: https://cutadapt.readthedocs.io/en/latest/index.html
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626 .. _`Illumina TruSeq Adapters De-Mystified`: http://tucf-genomics.tufts.edu/documents/protocols/TUCF_Understanding_Illumina_TruSeq_Adapters.pdf
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627
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628
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629 --------------------
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630
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631 **Galaxy Wrapper Development**
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632
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633 --------------------
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634
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635 Author: Lance Parsons <lparsons@princeton.edu>
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636
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637 ]]></help>
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638
10
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639 <citations>
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640 <citation type="bibtex">
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641 @article{marcel_cutadapt_2011,
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642 title = {Cutadapt removes adapter sequences from high-throughput sequencing reads},
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643 volume = {17},
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644 copyright = {Authors who publish with this journal agree to the following terms: Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal. Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal. Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access ).},
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645 url = {http://journal.embnet.org/index.php/embnetjournal/article/view/200},
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646 abstract = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
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647
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648 Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/},
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649 number = {1},
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650 urldate = {2011-08-02},
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651 journal = {EMBnet.journal},
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652 author = {Marcel, Martin},
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653 year = {2011},
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654 note = {When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from each read before read mapping. Previous solutions are either hard to use or do not offer required features, in particular support for color space data. As an easy to use alternative, we developed the command-line tool cutadapt, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features. Cutadapt, including its MIT-licensed source code, is available for download at http://code.google.com/p/cutadapt/},
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655 keywords = {Adapter removal;, fastq, MicroRNA, Sequencing, Small RNA, software},
01d94df2e32a planemo upload for repository https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper
lparsons
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656 file = {Cutadapt removes adapter sequences from high-throughput sequencing reads | Martin | EMBnet.journal:/Users/lparsons/Library/Application Support/Firefox/Profiles/thd2t4je.default/zotero/storage/ZXZT4PSE/200.html:text/html}
01d94df2e32a planemo upload for repository https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper
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657 }
01d94df2e32a planemo upload for repository https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper
lparsons
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658 </citation>
01d94df2e32a planemo upload for repository https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper
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659 </citations>
01d94df2e32a planemo upload for repository https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper
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660
0
8b064ea16722 Initial version with multiple adapter support
Lance Parsons <lparsons@princeton.edu>
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661 </tool>