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1 <tool id="trim_galore" name="Trim Galore" version="0.2.8">
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2 <!-- Wrapper compatible with Trim Galore version 0.2.8 -->
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0
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3 <description>adaptive quality and adapter trimmer</description>
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4 <version_command interpreter="perl">trim_galore --version</version_command>
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5 <requirements>
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6 <requirement type="package" version="1.1">cutadapt</requirement>
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7 </requirements>
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8 <command interpreter="perl">
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9 #from glob import glob
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10 #import tempfile, os
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1
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11
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12 ##
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13 ## Creating a temporary directory where trim_galore will store all result files
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14 ##
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15
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16 #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
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17
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18
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19 ## trim_galore removes .fastq and .fq file extensions of input files.
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20 ## That is essential if Galaxy provides links to files (these can have real extensions), but that behaviour is causing an inconsitency in output filenaming.
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21 ## Fix: link every file to $TMP without file extension
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22
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23 #if $singlePaired.sPaired == "single":
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24 #set $input_singles_tmp_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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25 #set $input_singles_tmp = $input_singles_tmp_handle.name
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26 #silent $input_singles_tmp_handle.close()
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27 #silent os.system("ln -s %s %s" % (str($singlePaired.input_singles), $input_singles_tmp))
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28 #else:
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29 #set $input_mate1_tmp_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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30 #set $input_mate2_tmp_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
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31
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32 #set $input_mate1_tmp = $input_mate1_tmp_handle.name
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33 #silent $input_mate1_tmp_handle.close()
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34
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35 #set $input_mate2_tmp = $input_mate2_tmp_handle.name
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36 #silent $input_mate2_tmp_handle.close()
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37
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38 #silent os.system("ln -s %s %s" % (str($singlePaired.input_mate1), $input_mate1_tmp))
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39 #silent os.system("ln -s %s %s" % (str($singlePaired.input_mate2), $input_mate2_tmp))
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40 #end if
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41
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0
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42 trim_galore
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43
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44 ##
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45 ## Input parameters
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46 ##
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47
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48
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49 #if $params.settingsType == "custom":
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50
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51 ## default 20
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52 --quality $params.quality
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53 ## default 'AGATCGGAAGAGC'
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54 #if $params.adapter.strip() != '':
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55 --adapter $params.adapter
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56 #end if
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57 ## default 1
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58 --stringency $params.stringency
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59
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60 ## default 0.1
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61 -e $params.error_rate
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62
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63 ## default 20
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64 --length $params.min_length
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65
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1
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66 #if int($params.clip_R1) > 0:
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67 --clip_R1 $params.clip_R1
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68 #end if
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69
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70 #if int($params.clip_R2) > 0:
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71 --clip_R2 $params.clip_R2
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72 #end if
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73
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0
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74 #if $params.retain_unpaired.settingsType == "retain_unpaired_output":
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75 --retain_unpaired
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76 --length_1 $params.retain_unpaired.length_1
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77 --length_2 $params.retain_unpaired.length_2
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78 #end if
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79
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80 #end if
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81
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82 ##
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83 ## RBBS specific options.
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84 ##
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85
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86 #if $rrbs.settingsType == "custom":
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87
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88 $rrbs.rrbs
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89 $rrbs.non_directional
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90
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91 #end if
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92
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93 --output_dir $temp_dir
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94 --suppress_warn
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95
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96
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97 #if $singlePaired.sPaired == "single":
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98
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99 #if $singlePaired.input_singles.ext == "fastqillumina":
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100 --phred64
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101 #elif $singlePaired.input_singles.ext == "fastqsanger":
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102 --phred33
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103 #end if
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104
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105 #if $params.settingsType == "custom":
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106 #if not $params.report:
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107 --no_report_file
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108 #end if
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109 #end if
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110
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111 ## input sequence
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1
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112 $input_singles_tmp
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113 #else:
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114 --paired
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115 #if $singlePaired.input_mate1.ext == "fastqillumina":
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116 --phred64
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117 #elif $singlePaired.input_mate1.ext == "fastqsanger":
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118 --phred33
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119 #end if
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120
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121 $singlePaired.trim1
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122 #if $singlePaired.adapter2.strip() != '':
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123 --adapter2 $singlePaired.adapter2
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124 #end if
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125
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126 #if $params.settingsType == "custom":
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127 #if not $params.report:
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128 --no_report_file
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129 #end if
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130 #end if
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131
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132 ## input sequences
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1
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133 $input_mate1_tmp
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134 $input_mate2_tmp
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135
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136 #end if
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137
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138 &&
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139
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140 ##
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141 ## Trim Galore! run is finished. Move the result files to the proper place
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142 ##
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143
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144
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145 #if $singlePaired.sPaired == "single":
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146 #set $single_end_path = os.path.join($temp_dir, os.path.basename(str($input_singles_tmp)) + '_trimmed.fq')
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147 mv $single_end_path $trimmed_reads_single;
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148
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149 #if $params.settingsType == "custom":
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150 #if $params.report:
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151 #set $report_path = os.path.join($temp_dir, os.path.basename(str($input_singles_tmp)) + '_trimming_report.txt')
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152 mv $report_path $report_file;
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153 #end if
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154 #end if
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155
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156 #else:
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157 #set $paired_end_path_1 = os.path.join($temp_dir, os.path.basename(str($input_mate1_tmp)) + '_val_1.fq')
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158 #set $paired_end_path_2 = os.path.join($temp_dir, os.path.basename(str($input_mate2_tmp)) + '_val_2.fq')
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159 mv $paired_end_path_1 $trimmed_reads_pair1;
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160 mv $paired_end_path_2 $trimmed_reads_pair2;
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161
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162 #if $params.settingsType == "custom":
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163 #if $params.retain_unpaired.settingsType == "retain_unpaired_output":
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1
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164 #set $unpaired_path_1 = os.path.join($temp_dir, os.path.basename(str($input_mate1_tmp)) + '_unpaired_1.fq')
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165 #set $unpaired_path_2 = os.path.join($temp_dir, os.path.basename(str($input_mate2_tmp)) + '_unpaired_2.fq')
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166 mv $unpaired_path_1 $unpaired_reads_1;
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167 mv $unpaired_path_2 $unpaired_reads_2;
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168 #end if
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169
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170 #if $params.report:
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171 #set $report_path = os.path.join($temp_dir, os.path.basename(str($input_mate1_tmp)) + '_trimming_report.txt')
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172 mv $report_path $report_file;
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173 #end if
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174
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175 #end if
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176 #end if
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177
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178 ## delete the temp_dir
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179 rm -rf $temp_dir
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180
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181 </command>
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182 <inputs>
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183
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184 <!-- Input Parameters -->
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185 <conditional name="singlePaired">
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186 <param name="sPaired" type="select" label="Is this library mate-paired?">
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187 <option value="single">Single-end</option>
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188 <option value="paired">Paired-end</option>
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189 </param>
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190 <when value="single">
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191 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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192 </when>
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193 <when value="paired">
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194 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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195 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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196 <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" />
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197 <param name="adapter2" type="text" value="" label="Optional adapter sequence to be trimmed off read 2">
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198 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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199 </param>
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200 </when>
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201 </conditional>
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202
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203
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204 <conditional name="params">
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205 <param name="settingsType" type="select" label="Trim galore! advanced settings" help="You can use the default settings or set custom values for any of Trim Galore's parameters.">
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206 <option value="default">Use Defaults</option>
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207 <option value="custom">Full parameter list</option>
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208 </param>
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209 <when value="default" />
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210 <!-- Full/advanced params. -->
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211 <when value="custom">
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212 <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal." help="For more information please see below." />
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213 <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed">
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214 <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator>
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215 </param>
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216 <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />
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217 <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />
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218 <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length INT" />
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219
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220 <param name="clip_R1" type="integer" value="0" label="nstructs Trim Galore to remove INT bp from the 5' end of read 1" />
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221 <param name="clip_R2" type="integer" value="0" label="nstructs Trim Galore to remove INT bp from the 5' end of read 2" />
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222
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223 <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />
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224
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225 <conditional name="retain_unpaired">
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226 <param name="settingsType" type="select" label="specify if you would like to retain unpaired reads">
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227 <option value="no_output">Do not output unpaired reads</option>
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228 <option value="retain_unpaired_output">Output unpaired reads</option>
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229 </param>
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230 <when value="no_output" />
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231 <!-- Output params. -->
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232 <when value="retain_unpaired_output">
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233 <param name="length_1" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 1 to be written" />
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234 <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" />
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235 </when> <!-- output -->
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236 </conditional> <!-- retain_unpaired -->
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237
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238 </when> <!-- full -->
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239 </conditional> <!-- params -->
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240
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241 <conditional name="rrbs">
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242 <param name="settingsType" type="select" label="RRBS specific settings">
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243 <option value="default">Use Defaults (no RRBS)</option>
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244 <option value="custom">Full parameter list</option>
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245 </param>
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246 <when value="default" />
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247 <!-- Full/advanced params. -->
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248 <when value="custom">
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249 <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True" label="Specifies that the input file was an MspI digested RRBS sample" />
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250 <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False" label="Selecting this option for non-directional RRBS libraries" />
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251 </when> <!-- full -->
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252 </conditional> <!-- params -->
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253
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254 </inputs>
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255 <outputs>
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256
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257 <data format="fastq" name="trimmed_reads_single" label="${tool.name} on ${on_string}: trimmed reads">
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258 <filter>singlePaired['sPaired'] == "single"</filter>
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259 <actions>
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260 <action type="format">
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261 <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
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262 </action>
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263 </actions>
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264 </data>
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265
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266 <data format="fastq" name="trimmed_reads_pair1" label="${tool.name} on ${on_string}: trimmed reads pair 1">
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267 <filter>singlePaired['sPaired'] == "paired"</filter>
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268 <actions>
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269 <action type="format">
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270 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
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271 </action>
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272 </actions>
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273 </data>
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274
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275 <data format="fastq" name="trimmed_reads_pair2" label="${tool.name} on ${on_string}: trimmed reads pair 2">
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276 <filter>singlePaired['sPaired'] == "paired"</filter>
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277 <actions>
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278 <action type="format">
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279 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
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280 </action>
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281 </actions>
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282 </data>
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283
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284 <data format="fastq" name="unpaired_reads_1" label="${tool.name} on ${on_string}: unpaired reads (1)">
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285 <filter>
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286 ((
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287 params['settingsType'] == "custom" and
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288 params['retain_unpaired']['settingsType'] == "retain_unpaired_output"
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289 ))
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290 </filter>
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291 <actions>
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292 <action type="format">
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293 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
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294 </action>
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295 </actions>
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296 </data>
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297
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298 <data format="fastq" name="unpaired_reads_2" label="${tool.name} on ${on_string}: unpaired reads (2)">
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299 <filter>
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300 ((
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301 params['settingsType'] == "custom" and
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302 params['retain_unpaired']['settingsType'] == "retain_unpaired_output"
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303 ))
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304 </filter>
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305 <actions>
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306 <action type="format">
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307 <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
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308 </action>
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309 </actions>
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310 </data>
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311
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312 <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file">
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313 <filter>
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314 ((
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315 params['settingsType'] == "custom" and
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316 params['report'] == True
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317 ))
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318 </filter>
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319 </data>
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320
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321 </outputs>
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322 <tests>
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323 </tests>
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324
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325 <help>
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326
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327 **What it does**
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328
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329 TrimGalore!_ is a wrapper script that makes use of the publically available
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2
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330 adapter trimming tool Cutadapt.
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0
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331
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332
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333 .. _TrimGalore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
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334
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335
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336 It is developed by Krueger F at the Babraham Institute.
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337
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338 ------
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339
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340
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341 </help>
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342 </tool>
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