annotate fastp.xml @ 1:f44e93b4529c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
author iuc
date Tue, 20 Mar 2018 04:24:38 -0400
parents 988729b728f0
children e0b44bf2543e
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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1 <tool id="fastp" name="fastp" version="@WRAPPER_VERSION@.0">
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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>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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6 <requirements>
988729b728f0 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>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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9 <version_command>fastp --version | tail -n 1</version_command>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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10 <command detect_errors="exit_code"><![CDATA[
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11 ## Link input files
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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13 #if $in1.is_of_type('fastq.gz')
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14 #set ext = 'fastq.gz'
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15 #else
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16 #set ext = 'fastq'
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17 #end if
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19 ln -s '$in1' input1.$ext &&
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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21 #if str($single_paired.single_paired_selector) == 'paired':
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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22 ln -s '$in2' input2.$ext &&
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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23 #end if
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1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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26 ## Set filename for output report
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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28 #import re
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29 #set $filename = re.sub('[^\w\-\s]', '_', str($in1.element_identifier))
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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31
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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32 ## Run fastp
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34 fastp
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1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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36 --thread \${GALAXY_SLOTS:-1}
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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37 --report_title 'fastp report for $filename'
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38
0
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39 #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'):
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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40 --phred64
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41 #end if
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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43 -i input1.$ext
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44 -o first.$ext
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46 #if str($single_paired.single_paired_selector) == 'paired':
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47 -I input2.$ext
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48 -O second.$ext
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49 #end if
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50
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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51
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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52 ## Adapter Trimming Options
0
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53
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54 $single_paired.adapter_trimming_options.disable_adapter_trimming
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55
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56 #if str($single_paired.adapter_trimming_options.adapter_sequence1):
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57 --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
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58 #end if
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59
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60 #if str($single_paired.single_paired_selector) == 'paired':
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61 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
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62 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
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63 #end if
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64 #end if
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66
1
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67 ## Global Trimming Options
0
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69 #if str($single_paired.global_trimming_options.trim_front1):
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70 -f $single_paired.global_trimming_options.trim_front1
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71 #end if
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73 #if str($single_paired.global_trimming_options.trim_tail1):
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74 -t $single_paired.global_trimming_options.trim_tail1
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75 #end if
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77 #if str($single_paired.single_paired_selector) == 'paired':
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78 #if str($single_paired.global_trimming_options.trim_front2):
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79 -F $single_paired.global_trimming_options.trim_front2
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80 #end if
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81 #if str($single_paired.global_trimming_options.trim_tail2):
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82 -T $single_paired.global_trimming_options.trim_tail2
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83 #end if
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84 #end if
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85
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86
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87 ## Overrepresented sequence analysis
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89 $overrepresented_sequence_analysis.overrepresentation_analysis
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90
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91 #if str($overrepresented_sequence_analysis.overrepresentation_sampling):
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92 -P $overrepresented_sequence_analysis.overrepresentation_sampling
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93 #end if
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94
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95
1
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96 ## Filter Options
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97
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98 ## Quality filtering options
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99
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100 $filter_options.quality_filtering_options.disable_quality_filtering
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101
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102 #if str($filter_options.quality_filtering_options.qualified_quality_phred):
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103 -q $filter_options.quality_filtering_options.qualified_quality_phred
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104 #end if
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105 #if str($filter_options.quality_filtering_options.unqualified_percent_limit):
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106 -u $filter_options.quality_filtering_options.unqualified_percent_limit
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107 #end if
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108 #if str($filter_options.quality_filtering_options.n_base_limit):
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109 -n $filter_options.quality_filtering_options.n_base_limit
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110 #end if
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111
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112
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113 ## Length filtering options
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114
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115 $filter_options.length_filtering_options.disable_length_filtering
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116
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117 #if str($filter_options.length_filtering_options.length_required):
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118 -l $filter_options.length_filtering_options.length_required
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119 #end if
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120
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121 ## Low complexity filtering options
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122
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123 $filter_options.low_complexity_filter.enable_low_complexity_filter
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124
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125 #if str($filter_options.low_complexity_filter.complexity_threshold):
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126 -Y $filter_options.low_complexity_filter.complexity_threshold
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127 #end if
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128
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129
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130 ## Read Modification Options
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131
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132 ## PolyG tail trimming, useful for NextSeq/NovaSeq data
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133
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134 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
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135 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
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136 --poly_g_min_len $read_mod_options.polyg_tail_trimming.poly_g_min_len
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137 #end if
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138 $read_mod_options.polyg_tail_trimming.trimming_select
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139 #end if
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140
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141 ## PolyX tail trimming
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142
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143 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
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144 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
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145 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
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146 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
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147 #end if
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148 #end if
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149
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150 ## UMI processing
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151
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152 #if $read_mod_options.umi_processing.umi:
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153 $read_mod_options.umi_processing.umi
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154 #if str($read_mod_options.umi_processing.umi_loc):
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155 --umi_loc '$read_mod_options.umi_processing.umi_loc'
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156 #end if
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157 #if str($read_mod_options.umi_processing.umi_len):
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158 --umi_len $read_mod_options.umi_processing.umi_len
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159 #end if
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160 #if str($read_mod_options.umi_processing.umi_prefix):
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161 --umi_prefix '$read_mod_options.umi_processing.umi_prefix'
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162 #end if
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163 #end if
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164
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165 ## Per read cutting by quality options
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166
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167 #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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168
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169 $read_mod_options.cutting_by_quality_options.cut_by_quality5
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170
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171 $read_mod_options.cutting_by_quality_options.cut_by_quality3
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172
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173 #if str($read_mod_options.cutting_by_quality_options.cut_window_size):
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174 -W $read_mod_options.cutting_by_quality_options.cut_window_size
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175 #end if
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176 #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):
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177 -M $read_mod_options.cutting_by_quality_options.cut_mean_quality
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178 #end if
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179 #end if
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180
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181 ## Base correction by overlap analysis options
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182
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183 $read_mod_options.base_correction_options.correction
0
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184
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185 &&
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186
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187 mv first.$ext '${out1}'
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188 #if str($single_paired.single_paired_selector) == 'paired':
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189 &&
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190 mv second.$ext '${out2}'
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191 #end if
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192 ]]></command>
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193 <inputs>
1
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194
0
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195 <conditional name="single_paired">
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196 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
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197 <option value="single" selected="true">Single-end</option>
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198 <option value="paired">Paired</option>
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199 </param>
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200 <when value="single">
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201 <expand macro="in1" />
1
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202 <section name="adapter_trimming_options" title="Adapter Trimming Options" expanded="False">
0
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203 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
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204 <expand macro="adapter_sequence1" />
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205 </section>
1
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206 <section name="global_trimming_options" title="Global Trimming Options" expanded="False">
0
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207 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
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208 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
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209 </section>
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210 </when>
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211 <when value="paired">
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212 <expand macro="in1" />
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213 <param name="in2" argument="-I" type="data" format="fastq,fastq.gz" optional="true" label="Input 2" help="Input FASTQ file #2."/>
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214 <section name="adapter_trimming_options" title="Adapter trimming options" expanded="False">
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215 <param name="disable_adapter_trimming" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Disable adapter trimming" help="Adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled."/>
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216 <expand macro="adapter_sequence1" />
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217 <param name="adapter_sequence2" argument="--adapter_sequence_r2" type="text" optional="true" label="Adapter sequence for input 2" help="The adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as adapter sequence value for input 1.">
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218 <sanitizer>
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219 <valid>
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220 <add value="A"/>
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221 <add value="T"/>
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222 <add value="C"/>
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223 <add value="G"/>
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224 </valid>
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225 </sanitizer>
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226 </param>
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227 </section>
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228 <section name="global_trimming_options" title="Global trimming options" expanded="False">
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229 <param name="trim_front1" argument="-f" type="integer" optional="true" label="Trim front for input 1" help="Trimming how many bases in front for read1, default is 0."/>
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230 <param name="trim_tail1" argument="-t" type="integer" optional="true" label="Trim tail for input 1" help="Trimming how many bases in tail for read1, default is 0."/>
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231 <param name="trim_front2" argument="-F" type="integer" optional="true" label="Trim front for input 2" help="Trimming how many bases in front for read2. If it's not specified, it will follow read1's settings."/>
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232 <param name="trim_tail2" argument="-T" type="integer" optional="true" label="Trim tail for input 2" help="Trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings."/>
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233 </section>
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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="Useful for NextSeq/NovaSeq data">
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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"/>
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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"/>
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313 </section>
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314 </inputs>
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315
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316 <outputs>
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317 <data name="out1" format_source="in1" label="${tool.name} on ${on_string}: Read 1 Output"/>
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318 <data name="out2" format_source="in2" label="${tool.name} on ${on_string}: Read 2 Output">
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319 <filter>single_paired['single_paired_selector'] == "paired"</filter>
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320 </data>
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321 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML Report">
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322 <filter>output_options['report_html'] is True</filter>
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323 </data>
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324 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON Report">
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325 <filter>output_options['report_json'] is True</filter>
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326 </data>
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327 </outputs>
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328
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329 <tests>
1
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330 <!-- Ensure default output works -->
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331 <test expect_num_outputs="2">
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332 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
0
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333 <param name="single_paired_selector" value="single"/>
1
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334 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
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335 <output name="report_html">
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336 <assert_contents>
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337 <has_text text="fastp report"/>
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338 </assert_contents>
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339 </output>
0
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340 </test>
1
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341 <!-- Ensure custom adapter works -->
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342 <test expect_num_outputs="2">
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343 <param name="in1" ftype="fastq" value="R1.fq"/>
0
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344 <param name="single_paired_selector" value="single"/>
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345 <param name="adapter_sequence1" value="ATCG"/>
1
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346 <output name="out1" ftype="fastq" file="out_a.fq"/>
0
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347 </test>
1
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348 <!-- Ensure UMI processing works -->
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349 <test expect_num_outputs="2">
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350 <param name="in1" ftype="fastq" value="R1.fq"/>
0
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351 <param name="single_paired_selector" value="single"/>
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352 <section name="umi_processing">
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353 <param name="umi" value="true"/>
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354 <param name="umi_loc" value="read1"/>
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355 <param name="umi_len" value="8"/>
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356 </section>
1
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357 <output name="out1" ftype="fastq" file="out2.fq"/>
0
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358 </test>
1
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359 <!-- Ensure UMI processing with different lengths works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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parents: 0
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360 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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361 <param name="in1" ftype="fastq" value="R1.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
362 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
363 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
364 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
365 <param name="umi_loc" value="read1"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
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366 <param name="umi_len" value="12"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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367 </section>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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368 <output name="out1" ftype="fastq" file="out3.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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369 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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370 <!-- Ensure paired-end fastq works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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371 <test expect_num_outputs="3">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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372 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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373 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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374 <param name="single_paired_selector" value="paired"/>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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375 <output name="out1" ftype="fastq" file="out_bwa1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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376 <output name="out2" ftype="fastq" file="out_bwa2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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377 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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378 <!-- Ensure paired-end UMI processing of Read 1 works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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379 <test expect_num_outputs="3">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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380 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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381 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.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
382 <param name="single_paired_selector" value="paired"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
383 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
384 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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385 <param name="umi_loc" value="read1"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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386 <param name="umi_len" value="8"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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387 </section>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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388 <output name="out1" ftype="fastq" file="out_bwa_umi_read1_1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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389 <output name="out2" ftype="fastq" 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
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390 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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391 <!-- Ensure paired-end UMI processing of Read 2 works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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392 <test expect_num_outputs="3">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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393 <param name="in1" ftype="fastq" value="bwa-mem-fastq1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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394 <param name="in2" ftype="fastq" value="bwa-mem-fastq2.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
395 <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
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diff changeset
396 <section name="umi_processing">
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
397 <param name="umi" value="true"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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398 <param name="umi_loc" value="read2"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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399 <param name="umi_len" value="8"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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400 </section>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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401 <output name="out1" ftype="fastq" file="out_bwa_umi_read2_1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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402 <output name="out2" ftype="fastq" file="out_bwa_umi_read2_2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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403 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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404 <!-- Ensure JSON report output works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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405 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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406 <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
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407 <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
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408 <param name="report_html" value="False"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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409 <param name="report_json" value="True"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
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410 <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
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411 <output name="report_json">
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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412 <assert_contents>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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413 <has_text text="fastp report"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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414 </assert_contents>
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415 </output>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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416 </test>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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417 <!-- Ensure polyG trimming works -->
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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418 <test expect_num_outputs="2">
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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419 <param name="in1" ftype="fastq.gz" value="R1.fq.gz"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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420 <param name="single_paired_selector" value="single"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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421 <param name="trimming_select" value="-g"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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422 <param name="poly_g_min_len" value="10"/>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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423 <output name="out1" ftype="fastq.gz" decompress="True" file="out1.fq.gz"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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424 </test>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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425 </tests>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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diff changeset
426 <help><![CDATA[
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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427 .. class:: infomark
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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428
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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429 **What it does**
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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430
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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431 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.
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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432
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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433 *Features*
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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434
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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435 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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436
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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diff changeset
437 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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438
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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439 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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440
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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diff changeset
441 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
iuc
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diff changeset
442
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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diff changeset
443 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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444
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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445 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
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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446
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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diff changeset
447 7. Preprocess unique molecular identifer (UMI) enabled data, shift UMI to sequence name
0
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448
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449 8. Report JSON format result for further interpreting
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450
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f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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451 9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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452
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f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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453 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*)
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988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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454
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455 11. Support long reads (data from PacBio / Nanopore devices)
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456
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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457 -----
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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458
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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459 **Inputs**
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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460
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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461 Single-end or Paired-end FASTQ or FASTQ.GZ reads
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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462
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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463 -----
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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464
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465 **Outputs**
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466
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467 * Processed reads
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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468
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469 Optionally, under **Output Options** you can choose to output
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470
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471 * HTML report (default is Yes)
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472 * JSON report
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473
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474 .. _fastp: https://github.com/OpenGene/fastp
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475
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476 ]]></help>
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477 <citations>
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478 <citation type="doi">10.1101/274100</citation>
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479 </citations>
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480 </tool>