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annotate fastp.xml @ 7:2fcdbf78caf9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 249269561e1d3a767371c154677e5dd59147f7d7
author iuc
date Wed, 16 Jan 2019 04:01:17 -0500
parents 7c49e331a737
children 1eb1895ab19c
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7
2fcdbf78caf9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 249269561e1d3a767371c154677e5dd59147f7d7
iuc
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1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@">
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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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>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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5 </macros>
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6 <requirements>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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7 <requirement type="package" version="@WRAPPER_VERSION@">fastp</requirement>
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8 </requirements>
3
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9 <version_command>fastp -v</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
20c09892cfe7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 761a954744119f6317afe28eb50bd4f3fdea4984
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12
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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13 ## Link input files
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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14
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15 #set ext = '.fastq'
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17 #if $single_paired.single_paired_selector == 'paired_collection':
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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18 #if $single_paired.paired_input.forward.is_of_type('fastq.gz'):
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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19 #set ext = '.fastq.gz'
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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20 #end if
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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21 #set $in1 = $single_paired.paired_input.forward
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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22 #set $in2 = $single_paired.paired_input.reverse
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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23 #set $in1_name = re.sub('[^\w\-\s]', '_', str($single_paired.paired_input.name)) + $ext
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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24 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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25 #set out1 = $output_paired_coll.forward
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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26 #set out2 = $output_paired_coll.reverse
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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27 ln -s '$in1' '$in1_name' &&
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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28 ln -s '$in2' '$in2_name' &&
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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29 #else
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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30 #if $in1.is_of_type('fastq.gz')
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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31 #set ext = '.fastq.gz'
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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32 #end if
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33
5
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34 #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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35 ln -s '$in1' '$in1_name' &&
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36
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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37 #if str($single_paired.single_paired_selector) == 'paired':
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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38 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_R2" % $in2.element_identifier)) + $ext
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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39 ln -s '$in2' '$in2_name' &&
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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40 #end if
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cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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41 #end if
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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44 ## Run fastp
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45
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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46 fastp
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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47
1
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48 --thread \${GALAXY_SLOTS:-1}
4
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49 --report_title 'fastp report for $in1_name'
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50
0
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51 #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
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52 --phred64
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53 #end if
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54
5
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55 -i '$in1_name'
4
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56 -o first${ext}
0
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57
5
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58 #if str($single_paired.single_paired_selector).startswith('paired'):
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59 -I '$in2_name'
4
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60 -O second${ext}
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61 #end if
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62
1
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63
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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64 ## Adapter Trimming Options
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65
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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66 $single_paired.adapter_trimming_options.disable_adapter_trimming
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67
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68 #if str($single_paired.adapter_trimming_options.adapter_sequence1):
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69 --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
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70 #end if
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71
5
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72 #if str($single_paired.single_paired_selector).startswith('paired'):
0
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73 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
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74 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
7
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75 #else
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76 --detect_adapter_for_pe
0
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77 #end if
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78 #end if
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cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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80
1
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81 ## Global Trimming Options
0
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82
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83 #if str($single_paired.global_trimming_options.trim_front1):
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84 -f $single_paired.global_trimming_options.trim_front1
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85 #end if
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86
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87 #if str($single_paired.global_trimming_options.trim_tail1):
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88 -t $single_paired.global_trimming_options.trim_tail1
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89 #end if
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90
5
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91 #if str($single_paired.single_paired_selector).startswith('paired'):
0
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92 #if str($single_paired.global_trimming_options.trim_front2):
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93 -F $single_paired.global_trimming_options.trim_front2
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94 #end if
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95 #if str($single_paired.global_trimming_options.trim_tail2):
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96 -T $single_paired.global_trimming_options.trim_tail2
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97 #end if
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98 #end if
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99
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100
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101 ## Overrepresented sequence analysis
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102
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103 $overrepresented_sequence_analysis.overrepresentation_analysis
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104
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105 #if str($overrepresented_sequence_analysis.overrepresentation_sampling):
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106 -P $overrepresented_sequence_analysis.overrepresentation_sampling
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107 #end if
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108
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109
1
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110 ## Filter Options
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111
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112 ## Quality filtering options
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113
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114 $filter_options.quality_filtering_options.disable_quality_filtering
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115
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116 #if str($filter_options.quality_filtering_options.qualified_quality_phred):
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117 -q $filter_options.quality_filtering_options.qualified_quality_phred
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118 #end if
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119 #if str($filter_options.quality_filtering_options.unqualified_percent_limit):
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120 -u $filter_options.quality_filtering_options.unqualified_percent_limit
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121 #end if
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122 #if str($filter_options.quality_filtering_options.n_base_limit):
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123 -n $filter_options.quality_filtering_options.n_base_limit
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124 #end if
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125
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126
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127 ## Length filtering options
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128
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129 $filter_options.length_filtering_options.disable_length_filtering
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130
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131 #if str($filter_options.length_filtering_options.length_required):
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132 -l $filter_options.length_filtering_options.length_required
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133 #end if
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134
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135 ## Low complexity filtering options
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136
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137 $filter_options.low_complexity_filter.enable_low_complexity_filter
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138
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139 #if str($filter_options.low_complexity_filter.complexity_threshold):
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140 -Y $filter_options.low_complexity_filter.complexity_threshold
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141 #end if
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142
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143
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144 ## Read Modification Options
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145
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146 ## PolyG tail trimming, useful for NextSeq/NovaSeq data
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147
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148 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
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149 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
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150 --poly_g_min_len $read_mod_options.polyg_tail_trimming.poly_g_min_len
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151 #end if
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152 $read_mod_options.polyg_tail_trimming.trimming_select
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153 #end if
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154
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155 ## PolyX tail trimming
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156
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157 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
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158 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
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159 #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len):
1
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160 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
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161 #end if
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162 #end if
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163
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164 ## UMI processing
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165
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166 #if $read_mod_options.umi_processing.umi:
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167 $read_mod_options.umi_processing.umi
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168 #if str($read_mod_options.umi_processing.umi_loc):
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169 --umi_loc '$read_mod_options.umi_processing.umi_loc'
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170 #end if
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171 #if str($read_mod_options.umi_processing.umi_len):
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172 --umi_len $read_mod_options.umi_processing.umi_len
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173 #end if
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174 #if str($read_mod_options.umi_processing.umi_prefix):
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175 --umi_prefix '$read_mod_options.umi_processing.umi_prefix'
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176 #end if
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177 #end if
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178
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179 ## Per read cutting by quality options
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180
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181 #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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182
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183 $read_mod_options.cutting_by_quality_options.cut_by_quality5
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184
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185 $read_mod_options.cutting_by_quality_options.cut_by_quality3
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186
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187 #if str($read_mod_options.cutting_by_quality_options.cut_window_size):
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188 -W $read_mod_options.cutting_by_quality_options.cut_window_size
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189 #end if
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190 #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):
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191 -M $read_mod_options.cutting_by_quality_options.cut_mean_quality
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192 #end if
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193 #end if
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194
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195 ## Base correction by overlap analysis options
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196
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197 $read_mod_options.base_correction_options.correction
0
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198
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199 &&
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200
4
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201 mv first${ext} '${out1}'
5
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202 #if str($single_paired.single_paired_selector).startswith('paired'):
0
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203 &&
4
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204 mv second${ext} '${out2}'
0
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205 #end if
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206 ]]></command>
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207 <inputs>
1
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208
0
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209 <conditional name="single_paired">
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210 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
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211 <option value="single" selected="true">Single-end</option>
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212 <option value="paired">Paired</option>
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213 <option value="paired_collection">Paired Collection</option>
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214 </param>
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215 <when value="single">
5
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216 <expand macro="in" />
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217 <expand macro="adapter_trimming_options" />
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218 <expand macro="global_trimming_options" />
0
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219 </when>
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220 <when value="paired">
5
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221 <expand macro="in" read_number="1" argument="-i"/>
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222 <expand macro="in" read_number="2" argument="-I"/>
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223 <expand macro="adapter_trimming_options">
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224 <expand macro="adapter_sequence" read_number="2"/>
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225 </expand>
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226 <expand macro="global_trimming_options_paired" />
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227 </when>
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228 <when value="paired_collection">
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229 <param name="paired_input" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Select paired collection(s)"/>
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230 <expand macro="adapter_trimming_options">
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231 <expand macro="adapter_sequence" read_number="2"/>
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232 </expand>
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233 <expand macro="global_trimming_options_paired" />
0
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234 </when>
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235 </conditional>
1
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236
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237 <section name="overrepresented_sequence_analysis" title="Overrepresented Sequence Analysis" expanded="False">
0
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238 <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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239 <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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240 </section>
1
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241
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242 <!-- Filter Options -->
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243 <section name="filter_options" title="Filter Options">
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244 <section name="quality_filtering_options" title="Quality filtering options" expanded="True">
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245 <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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246 <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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247 <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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248 <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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249 </section>
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250
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251 <section name="length_filtering_options" title="Length filtering options" expanded="True">
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252 <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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253 <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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254 </section>
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255
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256 <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
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257 <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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258 <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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259 </section>
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260 </section>
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261
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262 <!-- Read Modification Options -->
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263 <section name="read_mod_options" title="Read Modification Options">
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264 <conditional name="polyg_tail_trimming">
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265 <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.">
1
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266 <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option>
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267 <option value="-g">Force polyG tail trimming</option>
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268 <option value="-G">Disable polyG tail trimming</option>
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269 </param>
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270 <when value="-g">
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271 <expand macro="poly_g_min_len" />
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272 </when>
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273 <when value="">
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274 <expand macro="poly_g_min_len" />
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275 </when>
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276 <when value="-G" />
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277 </conditional>
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278
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279 <conditional name="polyx_tail_trimming">
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280 <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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281 <option value="" selected="true">Disable polyX trimming</option>
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282 <option value="-x">Enable polyX tail trimming</option>
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283 </param>
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284 <when value="-x">
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285 <param name="poly_x_min_len" argument="--poly_x_min_len" type="integer" optional="true" label="PolyX minimum length"
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286 help="The minimum length to detect polyX in the read tail. 10 by default."/>
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287 </when>
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288 <when value="" />
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289 </conditional>
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290
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291 <section name="umi_processing" title="UMI processing" expanded="True">
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292 <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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293 <param name="umi_loc" 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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294 <param name="umi_len" 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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295 <param name="umi_prefix" 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."/>
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296 </section>
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297
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298 <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">
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299 <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)."/>
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300 <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)."/>
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301 <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."/>
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302 <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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303 </section>
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304
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305 <section name="base_correction_options" title="Base correction by overlap analysis options" expanded="True">
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306 <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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307 </section>
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308 </section>
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309
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310 <section name="output_options" title="Output Options" expanded="False">
0
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311 <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"/>
4
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312 <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="False" 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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313 </section>
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314 </inputs>
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315
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316 <outputs>
5
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317 <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 Output">
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318 <filter>single_paired['single_paired_selector'] in ["single", "paired"]</filter>
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319 </data>
0
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320 <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 Output">
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321 <filter>single_paired['single_paired_selector'] == "paired"</filter>
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322 </data>
5
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323 <collection name="output_paired_coll" type="paired" structured_like="paired_input" inherit_format="true" label="Paired-end output of ${tool.name} on ${on_string}">
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324 <filter>single_paired['single_paired_selector'] == "paired_collection"</filter>
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325 </collection>
0
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326 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML Report">
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327 <filter>output_options['report_html'] is True</filter>
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328 </data>
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329 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON Report">
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330 <filter>output_options['report_json'] is True</filter>
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331 </data>
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332 </outputs>
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333
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334 <tests>
1
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335 <!-- Ensure default output works -->
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336 <test expect_num_outputs="2">
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337 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
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338 <param name="single_paired_selector" value="single"/>
1
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339 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
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340 <output name="report_html">
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341 <assert_contents>
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342 <has_text text="fastp report"/>
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343 </assert_contents>
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344 </output>
0
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345 </test>
5
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346 <!-- Ensure paired collection works -->
7
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347 <test expect_num_outputs="4">
5
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348 <param name="single_paired_selector" value="paired_collection"/>
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349 <param name="paired_input">
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350 <collection type="paired">
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351 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
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352 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
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353 </collection>
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354 </param>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
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355 <output name="report_html">
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
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356 <assert_contents>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
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357 <has_text text="fastp report"/>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
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358 </assert_contents>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
359 </output>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
360 <output_collection name="output_paired_coll" type="paired">
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
361 <element name="forward" value="out_bwa1.fq" ftype="fastqsanger"/>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
362 <element name="reverse" value="out_bwa2.fq" ftype="fastqsanger"/>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
363 </output_collection>
4c14c2f8f4fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
diff changeset
364 </test>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
365 <!-- Ensure custom adapter works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
366 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
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367 <param name="in1" ftype="fastq" value="R1.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
368 <param name="single_paired_selector" value="single"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
369 <param name="adapter_sequence1" value="ATCG"/>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
370 <output name="out1" ftype="fastq" file="out_a.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
371 </test>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
372 <!-- Ensure UMI processing works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
373 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
374 <param name="in1" ftype="fastq" value="R1.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
375 <param name="single_paired_selector" value="single"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
376 <section name="umi_processing">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
377 <param name="umi" value="true"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
378 <param name="umi_loc" value="read1"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
379 <param name="umi_len" value="8"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
380 </section>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
381 <output name="out1" ftype="fastq" file="out2.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
382 </test>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
383 <!-- Ensure UMI processing with different lengths works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
384 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
385 <param name="in1" ftype="fastq" value="R1.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
386 <param name="single_paired_selector" value="single"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
387 <section name="umi_processing">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
388 <param name="umi" value="true"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
389 <param name="umi_loc" value="read1"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
390 <param name="umi_len" value="12"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
391 </section>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
392 <output name="out1" ftype="fastq" file="out3.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
393 </test>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
394 <!-- Ensure paired-end fastq works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
395 <test expect_num_outputs="3">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
396 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
397 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
398 <param name="single_paired_selector" value="paired"/>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
399 <output name="out1" ftype="fastq" file="out_bwa1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
400 <output name="out2" ftype="fastq" file="out_bwa2.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
401 </test>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
402 <!-- Ensure paired-end UMI processing of Read 1 works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
403 <test expect_num_outputs="3">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
404 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
405 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
406 <param name="single_paired_selector" value="paired"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
407 <section name="umi_processing">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
408 <param name="umi" value="true"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
409 <param name="umi_loc" value="read1"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
410 <param name="umi_len" value="8"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
411 </section>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
412 <output name="out1" ftype="fastq" file="out_bwa_umi_read1_1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
413 <output name="out2" ftype="fastq" file="out_bwa_umi_read1_2.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
414 </test>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
415 <!-- Ensure paired-end UMI processing of Read 2 works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
416 <test expect_num_outputs="3">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
417 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
418 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
419 <param name="single_paired_selector" value="paired"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
420 <section name="umi_processing">
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
421 <param name="umi" value="true"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
422 <param name="umi_loc" value="read2"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
423 <param name="umi_len" value="8"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
424 </section>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
425 <output name="out1" ftype="fastq" file="out_bwa_umi_read2_1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
426 <output name="out2" ftype="fastq" file="out_bwa_umi_read2_2.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
427 </test>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
428 <!-- Ensure JSON report output works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
429 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
430 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
431 <param name="single_paired_selector" value="single"/>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
432 <param name="report_html" value="False"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
433 <param name="report_json" value="True"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
434 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
435 <output name="report_json">
0
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
436 <assert_contents>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
437 <has_text text="fastp report"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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diff changeset
438 </assert_contents>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
439 </output>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
440 </test>
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
441 <!-- Ensure polyG trimming works -->
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
442 <test expect_num_outputs="2">
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
443 <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>
0
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444 <param name="single_paired_selector" value="single"/>
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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445 <param name="trimming_select" value="-g"/>
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446 <param name="poly_g_min_len" value="10"/>
1
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447 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
0
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448 </test>
6
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449 <!-- Ensure polyX trimming works -->
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450 <test expect_num_outputs="2">
7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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451 <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>
7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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452 <param name="single_paired_selector" value="single"/>
7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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453 <param name="trimming_select" value="-G"/>
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454 <param name="polyx_trimming_select" value="-x"/>
7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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455 <param name="poly_x_min_len" value="10"/>
7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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456 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
7c49e331a737 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
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457 </test>
0
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458 </tests>
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459 <help><![CDATA[
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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460 .. class:: infomark
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461
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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462 **What it does**
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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463
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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464 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 afford high performance.
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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465
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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466 *Features*
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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467
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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468 1. Filter out bad reads (too low quality, too short, or too many N...)
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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469
1
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470 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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471
cb7226f7c585 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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472 3. Trim all reads in front and tail
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473
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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474 4. Cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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475
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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476 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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477
1
adf6b091b0a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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478 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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479
1
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480 7. Preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name
0
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481
1
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482 8. Report JSON format result for further interpreting
0
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483
1
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484 9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)
0
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485
1
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486 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 limitting the lines of each split file (*Not enabled in this Galaxy tool*)
0
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487
1
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488 11. Support long reads (data from PacBio / Nanopore devices)
0
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489
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490 -----
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491
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492 **Inputs**
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493
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494 Single-end or Paired-end FASTQ or FASTQ.GZ reads
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495
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496 -----
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497
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498 **Outputs**
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499
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500 * Processed reads
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501
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502 Optionally, under **Output Options** you can choose to output
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503
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504 * HTML report (default is Yes)
4
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505 * JSON report (compatible with MultiQC)
0
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506
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507 .. _fastp: https://github.com/OpenGene/fastp
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508
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509 ]]></help>
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510 <citations>
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511 <citation type="doi">10.1101/274100</citation>
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512 </citations>
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513 </tool>