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annotate fastp.xml @ 14:ecb9f4854617 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit b76fe0b833d61c5161ed033ce1f57e3881bf336f
author iuc
date Mon, 11 Nov 2024 14:53:41 +0000
parents dbfc505896e9
children
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ecb9f4854617 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit b76fe0b833d61c5161ed033ce1f57e3881bf336f
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1 <tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy0" profile="23.1">
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2 <description>fast all-in-one preprocessing for FASTQ files</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 <expand macro="biotools" />
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">fastp</requirement>
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9 </requirements>
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10 <version_command>fastp -v</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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14 ## Link input files
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16 #set ext = '.fastqsanger'
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17
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18 #if $single_paired.single_paired_selector == 'paired_collection'
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19 #if $single_paired.paired_input.forward.is_of_type('fastqsanger.gz')
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20 #set ext = '.fastqsanger.gz'
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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21 #elif $single_paired.paired_input.forward.is_of_type('fastqillumina.gz')
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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22 #set ext = '.fastqillumina.gz'
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23 #end if
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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24 #set $in1 = $single_paired.paired_input.forward
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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25 #set $in2 = $single_paired.paired_input.reverse
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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26 #set $in1_name = re.sub('[^\w\-\s]', '_', str($single_paired.paired_input.name)) + $ext
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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27 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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28 #set out1 = $output_paired_coll.forward
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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29 #set out2 = $output_paired_coll.reverse
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30 ln -sf '$in1' '$in1_name' &&
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
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31 ln -sf '$in2' '$in2_name' &&
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32 #else
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33 #if $in1.is_of_type('fastqsanger.gz')
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34 #set ext = '.fastqsanger.gz'
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35 #elif $in1.is_of_type('fastqillumina.gz')
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36 #set ext = '.fastqillumina.gz'
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37 #end if
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38
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39 #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
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40 ln -sf '$in1' '$in1_name' &&
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42 #if str($single_paired.single_paired_selector) == 'paired':
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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43 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_R2" % $in2.element_identifier)) + $ext
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44 ln -sf '$in2' '$in2_name' &&
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45 #end if
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46 #end if
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47
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48 cp '$c1' galaxy.json &&
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50 ## Run fastp
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52 fastp
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53
1
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54 --thread \${GALAXY_SLOTS:-1}
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55 --report_title 'fastp report for $in1_name'
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56
0
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57 #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
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58 --phred64
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59 #end if
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60
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61 -i '$in1_name'
0
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62
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63 ## Merge reads
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64
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65 #if str($single_paired.single_paired_selector).startswith('paired')
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66 -I '$in2_name'
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67 #if $single_paired.merge_reads.merge
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68 $single_paired.merge_reads.merge
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69 --merged_out '$merged_reads'
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70 #if $single_paired.merge_reads.include_unmerged
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71 $single_paired.merge_reads.include_unmerged
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72 #else
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73 --out1 '$unmerged_out1'
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74 --out2 '$unmerged_out2'
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75 --unpaired1 '$unpaired1'
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76 --unpaired2 '$unpaired2'
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77 #end if
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78 #else
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79 -o first${ext}
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80 -O second${ext}
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81 #end if
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82 #else
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83 -o first${ext}
0
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84 #end if
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85
1
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86 ## Adapter Trimming Options
0
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87
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88 $single_paired.adapter_trimming_options.disable_adapter_trimming
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89
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90 #if str($single_paired.adapter_trimming_options.adapter_sequence1):
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91 --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
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92 #end if
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93
5
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94 #if str($single_paired.single_paired_selector).startswith('paired'):
0
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95 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
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96 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
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97 #end if
12
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98 $single_paired.adapter_trimming_options.detect_adapter_for_pe
0
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99 #end if
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100
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101
1
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102 ## Global Trimming Options
0
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103
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104 #if str($single_paired.global_trimming_options.trim_front1):
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105 -f $single_paired.global_trimming_options.trim_front1
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106 #end if
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107
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108 #if str($single_paired.global_trimming_options.trim_tail1):
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109 -t $single_paired.global_trimming_options.trim_tail1
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110 #end if
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111
5
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112 #if str($single_paired.single_paired_selector).startswith('paired'):
0
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113 #if str($single_paired.global_trimming_options.trim_front2):
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114 -F $single_paired.global_trimming_options.trim_front2
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115 #end if
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116 #if str($single_paired.global_trimming_options.trim_tail2):
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117 -T $single_paired.global_trimming_options.trim_tail2
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118 #end if
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119 #end if
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120
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121
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122 ## Overrepresented sequence analysis
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123
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124 $overrepresented_sequence_analysis.overrepresentation_analysis
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125
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126 #if str($overrepresented_sequence_analysis.overrepresentation_sampling):
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127 -P $overrepresented_sequence_analysis.overrepresentation_sampling
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128 #end if
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129
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130
1
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131 ## Filter Options
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132
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133 ## Quality filtering options
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134
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135 $filter_options.quality_filtering_options.disable_quality_filtering
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136
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137 #if str($filter_options.quality_filtering_options.qualified_quality_phred):
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138 -q $filter_options.quality_filtering_options.qualified_quality_phred
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139 #end if
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140 #if str($filter_options.quality_filtering_options.unqualified_percent_limit):
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141 -u $filter_options.quality_filtering_options.unqualified_percent_limit
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142 #end if
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143 #if str($filter_options.quality_filtering_options.n_base_limit):
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144 -n $filter_options.quality_filtering_options.n_base_limit
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145 #end if
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146
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147
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148 ## Length filtering options
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149
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150 $filter_options.length_filtering_options.disable_length_filtering
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151
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152 #if str($filter_options.length_filtering_options.length_required):
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153 -l $filter_options.length_filtering_options.length_required
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154 #end if
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155
9
dbf9c561ef29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit a64eb7904f80e90a5faff04ea3fb797ee1e07d36"
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156 #if str($filter_options.length_filtering_options.length_limit):
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157 --length_limit $filter_options.length_filtering_options.length_limit
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158 #end if
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159
1
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160 ## Low complexity filtering options
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161
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162 $filter_options.low_complexity_filter.enable_low_complexity_filter
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163
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164 #if str($filter_options.low_complexity_filter.complexity_threshold):
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165 -Y $filter_options.low_complexity_filter.complexity_threshold
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166 #end if
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167
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168
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169 ## Read Modification Options
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170
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171 ## PolyG tail trimming, useful for NextSeq/NovaSeq data
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172
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173 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
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174 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
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175 --poly_g_min_len $read_mod_options.polyg_tail_trimming.poly_g_min_len
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176 #end if
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177 $read_mod_options.polyg_tail_trimming.trimming_select
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178 #end if
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179
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180 ## PolyX tail trimming
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181
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182 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
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183 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
6
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184 #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len):
1
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185 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
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186 #end if
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187 #end if
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188
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189 ## UMI processing
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190
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191 #if $read_mod_options.umi_processing.umi:
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192 $read_mod_options.umi_processing.umi
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193 #if str($read_mod_options.umi_processing.umi_loc):
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194 --umi_loc '$read_mod_options.umi_processing.umi_loc'
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195 #end if
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196 #if str($read_mod_options.umi_processing.umi_len):
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197 --umi_len $read_mod_options.umi_processing.umi_len
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198 #end if
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199 #if str($read_mod_options.umi_processing.umi_prefix):
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200 --umi_prefix '$read_mod_options.umi_processing.umi_prefix'
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201 #end if
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202 #end if
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203
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204 ## Per read cutting by quality options
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205
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206 #if $read_mod_options.cutting_by_quality_options.cut_by_quality5 or $read_mod_options.cutting_by_quality_options.cut_by_quality3:
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207
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208 $read_mod_options.cutting_by_quality_options.cut_by_quality5
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209
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210 $read_mod_options.cutting_by_quality_options.cut_by_quality3
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211
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212 #if str($read_mod_options.cutting_by_quality_options.cut_window_size):
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213 -W $read_mod_options.cutting_by_quality_options.cut_window_size
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214 #end if
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215 #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):
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216 -M $read_mod_options.cutting_by_quality_options.cut_mean_quality
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217 #end if
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218 #end if
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219
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220 ## Base correction by overlap analysis options
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221
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222 $read_mod_options.base_correction_options.correction
0
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223
13
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224 #if str($single_paired.single_paired_selector).startswith('single')
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225 &&
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226 mv first${ext} '${out1}'
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227 #elif str($single_paired.single_paired_selector).startswith('paired') and not $single_paired.merge_reads.merge:
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228 &&
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229 mv first${ext} '${out1}'
0
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230 &&
4
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231 mv second${ext} '${out2}'
0
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232 #end if
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233 ]]></command>
13
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234 <configfiles>
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235 <configfile name="c1">
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236 #set $ext1 = "fastqsanger"
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237 #set $ext2 = "fastqsanger"
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238 #if str($single_paired.single_paired_selector) == "single"
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239 #if $in1.ext.endswith("gz")
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240 #set $ext1 = "fastqsanger.gz"
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241 #end if
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242 #elif str($single_paired.single_paired_selector) == "paired"
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243 #if $in1.ext.endswith("gz")
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244 #set $ext1 = "fastqsanger.gz"
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245 #end if
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246 #if $in2.ext.endswith("gz")
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247 #set $ext2 = "fastqsanger.gz"
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248 #end if
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249 #else
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250 #if $paired_input.forward.ext.endswith("gz")
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251 #set $ext1 = "fastqsanger.gz"
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252 #end if
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253 #if $paired_input.reverse.ext.endswith("gz")
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254 #set $ext2 = "fastqsanger.gz"
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255 #end if
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256 #end if
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257 {
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258 "out1": {"ext": "$ext1"},
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259 "out2": {"ext": "$ext2"},
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260 "merged_reads": {"ext": "$ext1"},
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261 "unmerged_out1": {"ext": "$ext1"},
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262 "unmerged_out2": {"ext": "$ext2"},
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263 "unpaired1": {"ext": "$ext1"},
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264 "unpaired2": {"ext": "$ext2"}
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265 }
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266 </configfile>
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267 </configfiles>
0
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268 <inputs>
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269 <conditional name="single_paired">
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270 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
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271 <option value="single" selected="true">Single-end</option>
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272 <option value="paired">Paired</option>
5
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273 <option value="paired_collection">Paired Collection</option>
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274 </param>
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275 <when value="single">
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276 <expand macro="in" />
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277 <expand macro="adapter_trimming_options" />
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278 <expand macro="global_trimming_options" />
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279 </when>
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280 <when value="paired">
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281 <expand macro="in" read_number="1" argument="-i"/>
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282 <expand macro="in" read_number="2" argument="-I"/>
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283 <expand macro="merge_reads" />
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284 <expand macro="adapter_trimming_options">
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285 <expand macro="adapter_sequence" read_number="2"/>
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286 <expand macro="detect_adapter_for_pe" />
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287 </expand>
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288 <expand macro="global_trimming_options_paired" />
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289 </when>
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290 <when value="paired_collection">
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291 <param name="paired_input" type="data_collection" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz" label="Select paired collection(s)" collection_type="paired"/>
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292 <expand macro="merge_reads" />
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293 <expand macro="adapter_trimming_options">
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294 <expand macro="adapter_sequence" read_number="2"/>
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295 <expand macro="detect_adapter_for_pe" />
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296 </expand>
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297 <expand macro="global_trimming_options_paired" />
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298 </when>
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299 </conditional>
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300
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301 <section name="overrepresented_sequence_analysis" title="Overrepresented Sequence Analysis" expanded="False">
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302 <param name="overrepresentation_analysis" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Enable overrepresented analysis" help="Enable overrepresented sequence analysis."/>
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303 <param name="overrepresentation_sampling" argument="-P" type="integer" optional="true" label="Overrepresentation sampling" help="One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20."/>
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304 </section>
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305
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306 <!-- Filter Options -->
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307 <section name="filter_options" title="Filter Options">
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308 <section name="quality_filtering_options" title="Quality filtering options" expanded="True">
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309 <param name="disable_quality_filtering" argument="-Q" type="boolean" truevalue="-Q" falsevalue="" checked="false" label="Disable quality filtering" help="Quality filtering is enabled by default. If this option is specified, quality filtering is disabled."/>
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310 <param name="qualified_quality_phred" argument="-q" type="integer" optional="true" label="Qualified quality phred" help="The quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified."/>
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311 <param name="unqualified_percent_limit" argument="-u" type="integer" optional="true" label="Unqualified percent limit" help="How many percents of bases are allowed to be unqualified (0~100). Default 40 means 40%."/>
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312 <param name="n_base_limit" argument="-n" type="integer" optional="true" label="N base limit" help="If one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5."/>
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313 </section>
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314
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315 <section name="length_filtering_options" title="Length filtering options" expanded="True">
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316 <param name="disable_length_filtering" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Disable length filtering" help="Length filtering is enabled by default. If this option is specified, length filtering is disabled."/>
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317 <param name="length_required" argument="-l" type="integer" optional="true" label="Length required" help="Reads shorter than this value will be discarded. Default is 15."/>
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318 <param argument="--length_limit" type="integer" optional="true" label="Maximum length" help="Reads longer than this value will be discarded. Default is 0 and means no limitation."/>
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319 </section>
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320
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321 <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
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322 <param name="enable_low_complexity_filter" argument="-y" type="boolean" truevalue="-y" falsevalue="" checked="false" label="Enable low complexity filter" help="The complexity is defined as the percentage of base that is different from its next base, default is No"/>
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323 <param name="complexity_threshold" argument="-Y" type="integer" optional="true" label="Complexity threshold" help="Threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required."/>
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324 </section>
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325 </section>
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326
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327 <!-- Read Modification Options -->
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328 <section name="read_mod_options" title="Read Modification Options">
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329 <conditional name="polyg_tail_trimming">
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330 <param name="trimming_select" type="select" label="PolyG tail trimming" help="This feature is enabled for NextSeq/NovaSeq data by default. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records.">
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331 <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option>
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332 <option value="-g">Force polyG tail trimming</option>
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333 <option value="-G">Disable polyG tail trimming</option>
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334 </param>
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335 <when value="-g">
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336 <expand macro="poly_g_min_len" />
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337 </when>
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338 <when value="">
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339 <expand macro="poly_g_min_len" />
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340 </when>
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341 <when value="-G" />
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342 </conditional>
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343
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344 <conditional name="polyx_tail_trimming">
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345 <param name="polyx_trimming_select" type="select" label="PolyX tail trimming" help="Similar to polyG tail trimming. When polyG tail trimming and polyX tail trimming are both enabled, fastp will perform polyG trimming first, then perform polyX trimming. Disabled by default.">
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346 <option value="" selected="true">Disable polyX trimming</option>
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347 <option value="-x">Enable polyX tail trimming</option>
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348 </param>
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349 <when value="-x">
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350 <param argument="--poly_x_min_len" type="integer" optional="true" label="PolyX minimum length"
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351 help="The minimum length to detect polyX in the read tail. 10 by default."/>
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352 </when>
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353 <when value="" />
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354 </conditional>
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355
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356 <section name="umi_processing" title="UMI processing" expanded="True">
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357 <param name="umi" argument="-U" type="boolean" truevalue="-U" falsevalue="" checked="false" label="Enable unique molecular identifer" help="Enable unique molecular identifer (UMI) preprocessing."/>
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358 <param argument="--umi_loc" type="text" optional="true" label="UMI location" help="Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none."/>
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359 <param argument="--umi_len" type="integer" optional="true" label="UMI length" help="If the UMI is in read1/read2, its length should be provided."/>
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360 <param argument="--umi_prefix" type="text" optional="true" label="UMI prefix" help="If specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default."/>
1
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361 </section>
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362
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363 <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">
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364 <param name="cut_by_quality5" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false" label="Cut by quality in front (5')" help="Enable per read cutting by quality in front (5'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data)."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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365 <param name="cut_by_quality3" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false" label="Cut by quality in tail (3')" help="Enable per read cutting by quality in tail (3'), default is disabled (WARNING: this will interfere deduplication for SE data)."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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366 <param name="cut_window_size" argument="-W" type="integer" optional="true" label="Cutting window size" help="The size of the sliding window for sliding window trimming, default is 4."/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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367 <param name="cut_mean_quality" argument="-M" type="integer" optional="true" label="Cutting mean quality" help="The bases in the sliding window with mean quality below cutting_quality will be cut, default is Q20."/>
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368 </section>
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369
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370 <section name="base_correction_options" title="Base correction by overlap analysis options" expanded="True">
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371 <param name="correction" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Enable base correction" help="Enable base correction in overlapped regions (only for PE data), default is disabled."/>
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372 </section>
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373 </section>
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374
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375 <section name="output_options" title="Output Options" expanded="False">
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376 <param name="report_html" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output HTML report" help="fastp provides a QC report for the data Before and After filtering within a single HTML page, which enables comparison of the quality statistics changed by the preprocessing step directly"/>
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377 <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
0
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378 </section>
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379 </inputs>
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380
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381 <outputs>
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382 <data name="out1" format="auto" label="${tool.name} on ${on_string}: Read 1 output">
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383 <filter>single_paired['single_paired_selector'] in ["single", "paired"] and not single_paired['merge_reads']['merge']</filter>
5
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384 </data>
13
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385 <data name="out2" format="auto" label="${tool.name} on ${on_string}: Read 2 output">
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386 <filter>single_paired['single_paired_selector'] == "paired" and not single_paired['merge_reads']['merge']</filter>
0
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387 </data>
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388 <collection name="output_paired_coll" type="paired" format_source="paired_input['forward']" label="${tool.name} on ${on_string}: Paired-end output">
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389 <filter>single_paired['single_paired_selector'] == "paired_collection" and not single_paired['merge_reads']['merge']</filter>
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390 </collection>
8
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391 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML report">
0
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392 <filter>output_options['report_html'] is True</filter>
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393 </data>
8
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394 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON report">
0
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395 <filter>output_options['report_json'] is True</filter>
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396 </data>
13
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397 <data name="merged_reads" format="auto" label="${tool.name} on ${on_string}: Merged reads">
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398 <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge']</filter>
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399 </data>
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400 <data name="unmerged_out1" format="auto" label="${tool.name} on ${on_string}: Unmerged filtered reads1">
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401 <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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402 </data>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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403 <data name="unmerged_out2" format="auto" label="${tool.name} on ${on_string}: Unmerged filtered reads2">
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404 <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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405 </data>
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406 <data name="unpaired1" format="auto" label="${tool.name} on ${on_string}: Unmerged unfiltered reads1">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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407 <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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408 </data>
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409 <data name="unpaired2" format="auto" label="${tool.name} on ${on_string}: Unmerged unfiltered reads2">
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410 <filter>single_paired['single_paired_selector'] in ["paired", "paired_collection"] and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
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411 </data>
0
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412 </outputs>
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413
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414 <tests>
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415 <!-- 1. Ensure default output works -->
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416 <test expect_num_outputs="3">
1
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417 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
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418 <param name="single_paired_selector" value="single"/>
1
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419 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
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420 <output name="report_html">
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421 <assert_contents>
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422 <has_text text="fastp report"/>
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423 </assert_contents>
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424 </output>
13
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425 <output name="report_json">
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426 <assert_contents>
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427 <has_text text="fastp report"/>
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428 </assert_contents>
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429 </output>
0
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430 </test>
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431 <!-- 2. Ensure paired collection works -->
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432 <test expect_num_outputs="4">
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433 <param name="single_paired_selector" value="paired_collection"/>
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434 <param name="paired_input">
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435 <collection type="paired">
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436 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
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437 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
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438 </collection>
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diff changeset
439 </param>
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parents: 12
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440 <param name="report_json" value="False" />
5
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
441 <output name="report_html">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
442 <assert_contents>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
443 <has_text text="fastp report"/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
444 </assert_contents>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
445 </output>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
446 <output_collection name="output_paired_coll" type="paired">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
447 <element name="forward" value="out_bwa1.fq" ftype="fastqsanger"/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
448 <element name="reverse" value="out_bwa2.fq" ftype="fastqsanger"/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
449 </output_collection>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
450 </test>
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iuc
parents: 9
diff changeset
451 <!-- 3. Ensure custom adapter works -->
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
452 <test expect_num_outputs="2">
13
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iuc
parents: 12
diff changeset
453 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
454 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
455 <param name="adapter_sequence1" value="ATCG"/>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
456 <param name="report_json" value="False" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
457 <output name="out1" ftype="fastqsanger" file="out_a.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
458 </test>
11
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iuc
parents: 9
diff changeset
459 <!-- 4. Ensure UMI processing works -->
1
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iuc
parents: 0
diff changeset
460 <test expect_num_outputs="2">
13
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iuc
parents: 12
diff changeset
461 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
462 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
463 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
464 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
465 <param name="umi_loc" value="read1"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
466 <param name="umi_len" value="8"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
467 </section>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
468 <param name="report_json" value="False" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
469 <output name="out1" ftype="fastqsanger" file="out2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
470 </test>
11
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iuc
parents: 9
diff changeset
471 <!-- 5. Ensure UMI processing with different lengths works -->
1
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iuc
parents: 0
diff changeset
472 <test expect_num_outputs="2">
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
473 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
474 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
475 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
476 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
477 <param name="umi_loc" value="read1"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
478 <param name="umi_len" value="12"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
479 </section>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
480 <param name="report_json" value="False" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
481 <output name="out1" ftype="fastqsanger" file="out3.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
482 </test>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
483 <!-- 6. Ensure paired-end fastqsanger works -->
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
484 <test expect_num_outputs="3">
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
485 <param name="in1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
486 <param name="in2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
487 <param name="single_paired_selector" value="paired"/>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
488 <param name="report_json" value="False" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
489 <output name="out1" ftype="fastqsanger" file="out_bwa1.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
490 <output name="out2" ftype="fastqsanger" file="out_bwa2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
491 </test>
11
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
492 <!-- 7. Ensure paired-end UMI processing of Read 1 works -->
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
493 <test expect_num_outputs="3">
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
494 <param name="in1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
495 <param name="in2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
496 <param name="single_paired_selector" value="paired"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
497 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
498 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
499 <param name="umi_loc" value="read1"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
500 <param name="umi_len" value="8"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
501 </section>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
502 <param name="report_json" value="False" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
503 <output name="out1" ftype="fastqsanger" file="out_bwa_umi_read1_1.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
504 <output name="out2" ftype="fastqsanger" file="out_bwa_umi_read1_2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
505 </test>
11
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
506 <!-- 8. Ensure paired-end UMI processing of Read 2 works -->
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
507 <test expect_num_outputs="4">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
508 <param name="in1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
509 <param name="in2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
510 <param name="single_paired_selector" value="paired"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
511 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
512 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
513 <param name="umi_loc" value="read2"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
514 <param name="umi_len" value="8"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
515 </section>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
516 <output name="out1" ftype="fastqsanger" file="out_bwa_umi_read2_1.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
517 <output name="out2" ftype="fastqsanger" file="out_bwa_umi_read2_2.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
518 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
519 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
520 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
521 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
522 </output>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
523 </test>
11
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
524 <!-- 9. Ensure JSON report output works -->
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
525 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
526 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
527 <param name="single_paired_selector" value="single"/>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
528 <param name="report_html" value="False"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
529 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
530 <output name="report_json">
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
531 <assert_contents>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
532 <has_text text="fastp report"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
533 </assert_contents>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
534 </output>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
535 </test>
11
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
536 <!-- 10. Ensure polyG trimming works -->
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
537 <test expect_num_outputs="3">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
538 <param name="in1" ftype="fastqsanger.gz" value="R1.fq.gz"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
539 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
540 <param name="trimming_select" value="-g"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
541 <param name="poly_g_min_len" value="10"/>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
542 <output name="out1" ftype="fastqsanger.gz" decompress="True" file="out1.fq.gz"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
543 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
544 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
545 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
546 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
547 </output>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
548 </test>
11
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
549 <!-- 11. Ensure polyX trimming works -->
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
550 <test expect_num_outputs="3">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
551 <param name="in1" ftype="fastqsanger.gz" value="R1.fq.gz"/>
6
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
iuc
parents: 5
diff changeset
552 <param name="single_paired_selector" value="single"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
iuc
parents: 5
diff changeset
553 <param name="trimming_select" value="-G"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
iuc
parents: 5
diff changeset
554 <param name="polyx_trimming_select" value="-x"/>
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
iuc
parents: 5
diff changeset
555 <param name="poly_x_min_len" value="10"/>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
556 <output name="out1" ftype="fastqsanger.gz" decompress="True" file="out1.fq.gz"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
557 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
558 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
559 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
560 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
561 </output>
6
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
iuc
parents: 5
diff changeset
562 </test>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
563 <!-- 12. Test fastqsanger files with different length -->
11
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
564 <test expect_exit_code="255" expect_failure="true">
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
565 <param name="single_paired_selector" value="paired_collection"/>
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
566 <param name="paired_input">
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
567 <collection type="paired">
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
568 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
569 <element name="reverse" value="bwa-mem-fastq2_too_long.fq" ftype="fastqsanger" />
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
570 </collection>
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
571 </param>
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
572 </test>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
573 <!-- 13. Test merge reads in combination with paired -->
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
574 <test expect_num_outputs="5">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
575 <param name="in1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
576 <param name="in2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
577 <param name="single_paired_selector" value="paired"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
578 <param name="merge" value="--merge" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
579 <param name="report_html" value="False" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
580 <param name="report_json" value="False" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
581 <output name="merged_reads" ftype="fastqsanger" file="bwa-mem-merged-reads.fastqsanger" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
582 <output name="unmerged_out1" ftype="fastqsanger" file="bwa-mem-unmerged-filtered-reads1.fastqsanger" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
583 <output name="unmerged_out2" ftype="fastqsanger" file="bwa-mem-unmerged-filtered-reads2.fastqsanger" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
584 <output name="unpaired1" ftype="fastqsanger" file="bwa-mem-unmerged-unfiltered-reads1.fastqsanger" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
585 <output name="unpaired2" ftype="fastqsanger">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
586 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
587 <has_size size="0" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
588 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
589 </output>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
590 </test>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
591 <!-- 14. Test merge and include_unmerged in combination with paired collection -->
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
592 <test expect_num_outputs="2">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
593 <param name="single_paired_selector" value="paired_collection"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
594 <param name="paired_input">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
595 <collection type="paired">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
596 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
597 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
598 </collection>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
599 </param>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
600 <param name="merge" value="--merge" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
601 <param name="include_unmerged" value="--include_unmerged" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
602 <param name="report_html" value="False" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
603 <output name="merged_reads" ftype="fastqsanger" file="bwa-mem-merged-read-include-unmerged.fastqsanger" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
604 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
605 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
606 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
607 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
608 </output>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
609 </test>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
610 <!--15. Test paired collection in combination with compressed input-->
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
611 <test expect_num_outputs="4">
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612 <param name="single_paired_selector" value="paired_collection"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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613 <param name="paired_input">
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614 <collection type="paired">
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615 <element name="forward" value="bwa-mem-fastq-paired-collection/input_forward.fastqsanger.gz" ftype="fastqsanger.gz" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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616 <element name="reverse" value="bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz" ftype="fastqsanger.gz" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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617 </collection>
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618 </param>
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619 <param name="report_json" value="False" />
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620 <output name="report_html">
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621 <assert_contents>
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622 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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623 </assert_contents>
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624 </output>
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625 <output_collection name="output_paired_coll" type="paired">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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626 <element name="forward" value="bwa-mem-fastq-paired-collection/output_forward.fastqsanger.gz" decompress="True" ftype="fastqsanger.gz"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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627 <element name="reverse" value="bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz" decompress="True" ftype="fastqsanger.gz"/>
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628 </output_collection>
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629 </test>
0
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630 </tests>
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631 <help><![CDATA[
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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632 .. class:: infomark
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633
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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634 **What it does**
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635
11
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636 fastp_ is a tool designed to provide fast all-in-one preprocessing for FASTQ files. This tool is developed in C++ with multithreading supported to
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
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diff changeset
637 afford high performance.
0
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638
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
639 *Features*
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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640
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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641 1. Filter out bad reads (too low quality, too short, or too many N...)
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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642
1
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643 2. Cut low quality bases for per read in its 5' and 3' by evaluating the mean quality from a sliding window (like Trimmomatic but faster)
0
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644
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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645 3. Trim all reads in front and tail
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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646
1
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647 4. Cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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648
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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649 5. Correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra-low quality
0
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650
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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651 6. Trim polyG in 3' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)
0
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652
13
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653 7. Preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name
0
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654
1
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655 8. Report JSON format result for further interpreting
0
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656
1
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657 9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)
0
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658
13
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659 10. Split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limiting the lines of each split file (*Not enabled in this Galaxy tool*)
0
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660
1
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661 11. Support long reads (data from PacBio / Nanopore devices)
0
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662
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663 -----
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664
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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665 **Inputs**
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666
13
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667 Single-end or Paired-end (compressed) fastqsagnger or fastqillumina files
0
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668
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669 -----
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670
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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671 **Outputs**
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672
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673 * Processed reads
13
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674 * Merged reads
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675 * Unmerged filtered reads1, reads that cannot be merged successfully, but both pass all the filters.
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676 * Unmerged filtered reads2, reads that cannot be merged successfully, but both pass all the filters.
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677 * Unmerged unfiltered reads1, reads that cannot be merged, **read1** passes filters but **read2** doesn't.
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678 * Unmerged unfiltered reads2, reads that cannot be merged, **read2** passes filters but **read1** doesn't.
0
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679
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680 Optionally, under **Output Options** you can choose to output
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681
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682 * HTML report (default is Yes)
4
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683 * JSON report (compatible with MultiQC)
0
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684
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685 .. _fastp: https://github.com/OpenGene/fastp
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686
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687 ]]></help>
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688 <citations>
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689 <citation type="doi">10.1101/274100</citation>
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690 </citations>
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691 </tool>