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1 <tool id="prinseq_trimmer" name="FASTQ trimmer" version="0.1">
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2 <description>(prinseq)</description>
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3 <version_command interpreter="perl">prinseq-lite.pl --version</version_command>
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4 <requirements>
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5 <requirement type="package" version="0.20.3">prinseq_perl_dependencies</requirement>
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6 <requirement type="set_environment">PRINSEQ_SCRIPT_PATH</requirement>
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7 </requirements>
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8 <command>
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9 #import os
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10 temp_graph_file = `mktemp`;
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11
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12 perl \$PRINSEQ_SCRIPT_PATH/prinseq-lite.pl
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13 #if $seq_type.seq_type_opt == 'single':
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14 -fastq $seq_type.input_singles
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15 #if $seq_type.input_singles.ext == 'fastqillumina':
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16 -phred64
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17 #end if
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18 #else:
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19 -fastq $seq_type.input_mate1
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20 -fastq2 $seq_type.input_mate2
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21 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
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22 #import sys
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23 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )
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24 #end if
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25 #if $seq_type.input_mate1.ext == 'fastqillumina':
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26 -phred64
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27 -endif
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28 #end if
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29
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30 -out_good 'trimmed_reads'
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31 ## we do not use the filter options in prinseq, so we are not interested in reads
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32 ## that do not pass the filters
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33 -out_bad null
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34
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35 ## Trim options
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36 #if $trim_to_len:
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37 -trim_to_len $trim_to_len
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38 #end if
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39
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40 #if $trim_left:
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41 -trim_left $trim_left
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42 #end if
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43
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44 #if $trim_right:
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45 -trim_right
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46 #end if
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47
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48 #if $trim_qual_left or $trim_qual_right:
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49 -trim_qual_type $trim_qual_type
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50 -trim_qual_rule $trim_qual_rule
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51 -trim_qual_window $trim_qual_window
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52 -trim_qual_step $trim_qual_step
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53 #end if
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54
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55 #if $trim_qual_left:
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56 -trim_qual_left $trim_qual_left
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57 #end if
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58
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59 #if $trim_qual_right:
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60 -trim_qual_right $trim_qual_right
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61 #end if
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62
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63
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64 -graph_stats #echo ','.join( $graph_stats )#
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65
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66 ## summary are written to stdout
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67 -stats_all
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68
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69
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70 -graph_data $temp_graph_file
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71
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72 ;
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73
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74 perl \$PRINSEQ_SCRIPT_PATH/prinseq-graphs-noPCA.pl -i $temp_graph_file -html_all -o #echo os.path.join( $html_file.files_path, 'graphs' )#
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75
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76 ;
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77
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78 python \$PRINSEQ_SCRIPT_PATH/create_index.py $html_file.files_path > $html_file
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79
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80
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81 </command>
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82 <inputs>
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83 <conditional name="seq_type">
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84 <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
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85 <option value="single">Single-end</option>
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86 <option value="paired">Paired-end</option>
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87 </param>
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88 <when value="single">
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89 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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90 </when>
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91 <when value="paired">
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92 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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93 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
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94 </when>
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95 </conditional>
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96
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97 <param name="trim_to_len" type="integer" value=""
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98 label="Trim all sequence from the 3'-end to result in sequence with this length"
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99 help="(-trim_to_len)"/>
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100
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101 <param name="trim_left" type="integer" value=""
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102 label="Trim sequence at the 5'-end by trim_left positions"
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103 help="(-trim_left)"/>
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104
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105 <param name="trim_right" type="integer" value=""
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106 label="Trim sequence at the 3'-end by trim_right positions"
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107 help="(-trim_right)"/>
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108
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109 <param name="trim_left_p" type="integer" value=""
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110 label="Trim sequence at the 5'-end by trim_left_p percentage of read length."
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111 help="The trim length is rounded towards the lower integer (e.g. 143.6 is rounded to 143 positions). Use an integer between 1 and 100 for the percentage value. (-trim_left_p)"/>
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112
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113 <param name="trim_right_p" type="integer" value=""
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114 label="Trim sequence at the 3'-end by trim_right_p percentage of read length"
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115 help="The trim length is rounded towards the lower integer (e.g. 143.6 is rounded to 143 positions). Use an integer between 1 and 100 for the percentage value. (-trim_right_p)"/>
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116
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117 <param name="trim_tail_left" type="integer" value=""
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118 label="Trim poly-A/T tail with a minimum length of trim_tail_left at the 5'-end"
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119 help="(-trim_tail_left)"/>
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120
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121 <param name="trim_tail_right" type="integer" value=""
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122 label="Trim poly-A/T tail with a minimum length of trim_tail_right at the 3'-end"
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123 help="(-trim_tail_right)"/>
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124
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125 <param name="trim_ns_left" type="integer" value=""
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126 label="Trim poly-N tail with a minimum length of trim_ns_left at the 5'-end"
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127 help="(-trim_left)"/>
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128
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129 <param name="trim_ns_right" type="integer" value=""
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130 label="Trim poly-N tail with a minimum length of trim_ns_right at the 3'-end."
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131 help="(-trim_ns_right)"/>
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132
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133
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134 <param name="trim_qual_left" type="integer" value=""
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135 label=" Trim sequence by quality score from the 5'-end with this threshold score"
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136 help="(-trim_qual_left)"/>
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137
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138 <param name="trim_qual_right" type="integer" value=""
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139 label="Trim sequence by quality score from the 3'-end with this threshold score"
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140 help="(-trim_qual_right)"/>
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141
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142 <param name="trim_qual_type" type="select" label="Type of quality score calculation to use">
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143 <option value="min" selected="True">min</option>
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144 <option value="mean">mean</option>
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145 <option value="max">max</option>
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146 <option value="sum">sum</option>
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147 </param>
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148
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149 <param name="trim_qual_rule" type="select" label="Rule to use to compare quality score to calculated value.">
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150 <option value="gt">greater than quality score</option>
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151 <option value="lt" selected="True">less than quality score</option>
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152 <option value="et">equal to quality score</option>
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153 </param>
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154
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155 <param name="trim_qual_window" type="integer" value="1"
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156 label="The sliding window size used to calculate quality score by type"
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157 help="(-trim_qual_window)"/>
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158
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159 <param name="trim_qual_step" type="integer" value="1"
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160 label="Step size used to move the sliding window"
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161 help="To move the window over all quality scores without missing any, the step size should be less or equal to the window size(-trim_qual_step)"/>
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162
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163 <param name="graph_stats" type="select" multiple="True" label="Which statistics should be calculated included in the graph_data file">
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164 <option value="ld" selected="True">Length distribution</option>
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165 <option value="gc" selected="True">GC content distribution</option>
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166 <option value="qd" selected="True">Base quality distribution</option>
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167 <option value="ns" selected="True">Occurence of N</option>
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168 <option value="pt" selected="True">Poly-A/T tails</option>
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169 <option value="ts" selected="True">Tag sequence check</option>
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170 <option value="as" selected="True">Assembly quality measure</option>
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171 <option value="de" selected="True">Sequence duplication - exact only</option>
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172 <option value="da" selected="True">Sequence duplication - exact + 5'/3'</option>
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173 <option value="sc" selected="True">Sequence complexity</option>
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174 <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option>
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175 </param>
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176
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177
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178 <!-- TODO
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179 -log <file>
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180 Log file to keep track of parameters, errors, etc. The log file
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181 name is optional. If no file name is given, the log file name
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182 will be "inputname.log". If the log file already exists, new
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183 content will be added to the file.
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184 -->
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185
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186
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187 <outputs>
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188 <data format="fastq" name="ofile_single" metadata_source="seq_type.input_singles" label="${tool.name} on ${on_string}">
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189 <filter>seq_type['seq_type_opt'] == "single"</filter>
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190 </data>
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191
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192 <data format="fastq" name="outfile_r1" label="${tool.name} on ${on_string}">
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193 <filter>seq_type['seq_type_opt'] == "paired"</filter>
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194 <actions>
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195 <conditional name="seq_type.seq_type_opt">
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196 <when value="single">
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197 <action type="format">
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198 <option type="from_param" name="seq_type.input_singles" param_attribute="ext" />
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199 </action>
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200 </when>
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201 <when value="paired">
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202 <action type="format">
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203 <option type="from_param" name="seq_type.input_mate1" param_attribute="ext" />
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204 </action>
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205 </when>
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206 </conditional>
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207 </actions>
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208 </data>
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209 <data format="fastq" name="outfile_r2" label="${tool.name} on ${on_string}">
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210 <filter>seq_type['seq_type_opt'] == "paired"</filter>
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211 <actions>
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212 <conditional name="seq_type.seq_type_opt">
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213 <when value="single">
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214 <action type="format">
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215 <option type="from_param" name="seq_type.input_singles" param_attribute="ext" />
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216 </action>
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217 </when>
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218 <when value="paired">
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219 <action type="format">
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220 <option type="from_param" name="seq_type.input_mate1" param_attribute="ext" />
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221 </action>
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222 </when>
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223 </conditional>
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224 </actions>
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225 </data>
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226
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227 <data format="html" name="html_file" label="${tool.name} on ${on_string} summary" />
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228 </outputs>
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229 <tests>
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230 <test>
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231 <!-- grep a FASTA file for sequences with specific motif -->
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232 <param name="seq_type.input_singles" value="example1.fastq" />
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233 <output name="ofile_single" file="example1_trim_right_10.fastq" />
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234 <param name="trim_right" value="10" />
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235 </test>
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236 </tests>
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237 <help>
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238
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239
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240 .. class:: warningmark
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241
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242 **TIP**
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243
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244 -----
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245
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246 **What it does**
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247
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248
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249 PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data.
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250
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251
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252 http://prinseq.sourceforge.net/manual.html
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253
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254
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255 ***** ORDER OF PROCESSING *****
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256 The available options are processed in the following order:
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257
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258 seq_num, trim_left, trim_right, trim_left_p, trim_right_p,
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259 trim_qual_left, trim_qual_right, trim_tail_left,
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260 trim_tail_right, trim_ns_left, trim_ns_right, trim_to_len,
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261 min_len, max_len, range_len, min_qual_score, max_qual_score,
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262 min_qual_mean, max_qual_mean, min_gc, max_gc, range_gc,
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263 ns_max_p, ns_max_n, noniupac, lc_method, derep, seq_id,
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264 seq_case, dna_rna, out_format
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265
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266
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267
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268
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269 </help>
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270 </tool>
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