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annotate fastp.xml @ 16:10678d49d39e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
author iuc
date Sat, 08 Feb 2025 15:15:16 +0000
parents a626e8c0e1ba
children
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10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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1 <tool id="fastp" name="fastp" version="@TOOL_VERSION@+galaxy4" profile="23.1">
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2 <description>fast all-in-one preprocessing for FASTQ files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="biotools" />
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">fastp</requirement>
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9 </requirements>
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10 <version_command>fastp -v</version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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14 ## Link input files
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15
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16 #set ext = '.fastqsanger'
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18 #if $single_paired.single_paired_selector == 'paired_collection'
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19 #if $single_paired.paired_input.forward.is_of_type('fastqsanger.gz')
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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20 #set ext = '.fastqsanger.gz'
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21 #end if
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22 #set $in1 = $single_paired.paired_input.forward
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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23 #set $in2 = $single_paired.paired_input.reverse
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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24 #set $in1_name = re.sub('[^\w\-\s]', '_', str($single_paired.paired_input.name)) + $ext
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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25 #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext
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26 ln -sf '$in1' '$in1_name' &&
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
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27 ln -sf '$in2' '$in2_name' &&
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28 #else
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29 #if $in1.is_of_type('fastqsanger.gz')
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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30 #set ext = '.fastqsanger.gz'
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31 #end if
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32
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33 #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext
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34 ln -sf '$in1' '$in1_name' &&
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35 #end if
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37 ## Run fastp
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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39 fastp
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40
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41 --thread \${GALAXY_SLOTS:-1}
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42 --report_title 'fastp report for $in1_name'
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44 -i '$in1_name'
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45
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46 ## Merge reads
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47
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48 #if str($single_paired.single_paired_selector).startswith('paired')
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49 -I '$in2_name'
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50 #if $single_paired.merge_reads.merge
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51 $single_paired.merge_reads.merge
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52 --merged_out merged${ext}
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53 #if $single_paired.merge_reads.include_unmerged
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54 $single_paired.merge_reads.include_unmerged
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55 #else
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56 --out1 'unmerged_R1${ext}'
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57 --out2 'unmerged_R2${ext}'
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58 --unpaired1 'unpaired_R1${ext}'
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59 --unpaired2 'unpaired_R2${ext}'
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60 #end if
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61 #else
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62 -o first${ext}
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63 -O second${ext}
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64 #end if
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65 #else
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66 -o first${ext}
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67 #end if
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68
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69 ## Adapter Trimming Options
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71 $single_paired.adapter_trimming_options.disable_adapter_trimming
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73 #if str($single_paired.adapter_trimming_options.adapter_sequence1):
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74 --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1'
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75 #end if
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76
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77 #if str($single_paired.single_paired_selector).startswith('paired'):
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78 #if str($single_paired.adapter_trimming_options.adapter_sequence2):
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79 --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2'
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80 #end if
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81 $single_paired.adapter_trimming_options.detect_adapter_for_pe
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82 #end if
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84
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85 ## Global Trimming Options
0
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87 #if str($single_paired.global_trimming_options.trim_front1):
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88 -f $single_paired.global_trimming_options.trim_front1
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89 #end if
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90
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91 #if str($single_paired.global_trimming_options.trim_tail1):
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92 -t $single_paired.global_trimming_options.trim_tail1
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93 #end if
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94
5
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
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95 #if str($single_paired.single_paired_selector).startswith('paired'):
0
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96 #if str($single_paired.global_trimming_options.trim_front2):
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97 -F $single_paired.global_trimming_options.trim_front2
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98 #end if
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99 #if str($single_paired.global_trimming_options.trim_tail2):
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100 -T $single_paired.global_trimming_options.trim_tail2
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101 #end if
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102 #end if
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103
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104
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105 ## Overrepresented sequence analysis
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106
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107 $overrepresented_sequence_analysis.overrepresentation_analysis
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108
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109 #if str($overrepresented_sequence_analysis.overrepresentation_sampling):
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110 -P $overrepresented_sequence_analysis.overrepresentation_sampling
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111 #end if
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112
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113
1
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114 ## Filter Options
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115
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116 ## Quality filtering options
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117
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118 $filter_options.quality_filtering_options.disable_quality_filtering
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119
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120 #if str($filter_options.quality_filtering_options.qualified_quality_phred):
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121 -q $filter_options.quality_filtering_options.qualified_quality_phred
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122 #end if
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123 #if str($filter_options.quality_filtering_options.unqualified_percent_limit):
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124 -u $filter_options.quality_filtering_options.unqualified_percent_limit
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125 #end if
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126 #if str($filter_options.quality_filtering_options.n_base_limit):
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127 -n $filter_options.quality_filtering_options.n_base_limit
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128 #end if
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129
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130
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131 ## Length filtering options
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132
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133 $filter_options.length_filtering_options.disable_length_filtering
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134
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135 #if str($filter_options.length_filtering_options.length_required):
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136 -l $filter_options.length_filtering_options.length_required
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137 #end if
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138
9
dbf9c561ef29 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit a64eb7904f80e90a5faff04ea3fb797ee1e07d36"
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139 #if str($filter_options.length_filtering_options.length_limit):
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140 --length_limit $filter_options.length_filtering_options.length_limit
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141 #end if
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142
1
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143 ## Low complexity filtering options
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144
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145 $filter_options.low_complexity_filter.enable_low_complexity_filter
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146
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147 #if str($filter_options.low_complexity_filter.complexity_threshold):
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148 -Y $filter_options.low_complexity_filter.complexity_threshold
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149 #end if
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150
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151
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152 ## Read Modification Options
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153
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154 ## PolyG tail trimming, useful for NextSeq/NovaSeq data
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155
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156 #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']:
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157 #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len):
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158 --poly_g_min_len $read_mod_options.polyg_tail_trimming.poly_g_min_len
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159 #end if
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160 $read_mod_options.polyg_tail_trimming.trimming_select
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161 #end if
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162
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163 ## PolyX tail trimming
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164
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165 #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x':
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166 $read_mod_options.polyx_tail_trimming.polyx_trimming_select
6
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167 #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len):
1
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168 --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len
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169 #end if
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170 #end if
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171
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172 ## UMI processing
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173
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174 #if $read_mod_options.umi_processing.umi:
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175 $read_mod_options.umi_processing.umi
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176 #if str($read_mod_options.umi_processing.umi_loc):
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177 --umi_loc '$read_mod_options.umi_processing.umi_loc'
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178 #end if
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179 #if str($read_mod_options.umi_processing.umi_len):
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180 --umi_len $read_mod_options.umi_processing.umi_len
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181 #end if
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182 #if str($read_mod_options.umi_processing.umi_prefix):
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183 --umi_prefix '$read_mod_options.umi_processing.umi_prefix'
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184 #end if
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185 #end if
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186
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187 ## Per read cutting by quality options
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188
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189 #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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190
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191 $read_mod_options.cutting_by_quality_options.cut_by_quality5
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192
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193 $read_mod_options.cutting_by_quality_options.cut_by_quality3
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194
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195 #if str($read_mod_options.cutting_by_quality_options.cut_window_size):
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196 -W $read_mod_options.cutting_by_quality_options.cut_window_size
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197 #end if
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198 #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality):
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199 -M $read_mod_options.cutting_by_quality_options.cut_mean_quality
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200 #end if
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201 #end if
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202
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203 ## Base correction by overlap analysis options
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204
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205 $read_mod_options.base_correction_options.correction
0
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206
16
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207 #if str($single_paired.single_paired_selector) == 'paired_collection'
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208 #if $single_paired.merge_reads.merge
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209 && mv merged${ext} '$merged_reads'
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210 #if not $single_paired.merge_reads.include_unmerged
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211 && mv 'unmerged_R1${ext}' '$unmerged_out_coll.forward'
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212 && mv 'unmerged_R2${ext}' '$unmerged_out_coll.reverse'
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213 && mv 'unpaired_R1${ext}' '$unpaired_out_coll.forward'
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214 && mv 'unpaired_R2${ext}' '$unpaired_out_coll.reverse'
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215 #end if
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216 #else
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217 && mv first${ext} '$output_paired_coll.forward'
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218 && mv second${ext} '$output_paired_coll.reverse'
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219 #end if
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220 #else
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221 && mv first${ext} '${out1}'
0
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222 #end if
16
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223
0
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224 ]]></command>
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225 <inputs>
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226 <conditional name="single_paired">
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227 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
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228 <option value="single" selected="true">Single-end</option>
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229 <option value="paired_collection">Paired Collection</option>
0
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230 </param>
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231 <when value="single">
5
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232 <expand macro="in" />
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233 <expand macro="adapter_trimming_options" />
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234 <expand macro="global_trimming_options" />
0
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235 </when>
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236 <when value="paired_collection">
15
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237 <param name="paired_input" type="data_collection" format="fastqsanger,fastqsanger.gz" label="Select paired collection(s)" collection_type="paired"/>
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238 <expand macro="merge_reads" />
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239 <expand macro="adapter_trimming_options">
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240 <expand macro="adapter_sequence" read_number="2"/>
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241 <expand macro="detect_adapter_for_pe" />
5
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242 </expand>
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243 <expand macro="global_trimming_options_paired" />
0
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244 </when>
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245 </conditional>
1
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246
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247 <section name="overrepresented_sequence_analysis" title="Overrepresented Sequence Analysis" expanded="False">
0
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248 <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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249 <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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250 </section>
1
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251
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252 <!-- Filter Options -->
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253 <section name="filter_options" title="Filter Options">
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254 <section name="quality_filtering_options" title="Quality filtering options" expanded="True">
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255 <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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256 <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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257 <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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258 <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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259 </section>
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260
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261 <section name="length_filtering_options" title="Length filtering options" expanded="True">
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262 <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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263 <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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264 <param argument="--length_limit" type="integer" optional="true" label="Maximum length" help="Reads longer than this value will be discarded. Default is 0 and means no limitation."/>
1
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265 </section>
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266
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267 <section name="low_complexity_filter" title="Low complexity filtering options" expanded="True">
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268 <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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269 <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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270 </section>
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271 </section>
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272
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273 <!-- Read Modification Options -->
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274 <section name="read_mod_options" title="Read Modification Options">
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275 <conditional name="polyg_tail_trimming">
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276 <param name="trimming_select" type="select" label="PolyG tail trimming" help="This feature is enabled for NextSeq/NovaSeq data by default. NextSeq/NovaSeq data is detected by the machine ID in the FASTQ records.">
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277 <option value="" selected="true">Automatic trimming for Illumina NextSeq/NovaSeq data</option>
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278 <option value="-g">Force polyG tail trimming</option>
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279 <option value="-G">Disable polyG tail trimming</option>
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280 </param>
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281 <when value="-g">
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282 <expand macro="poly_g_min_len" />
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283 </when>
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284 <when value="">
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285 <expand macro="poly_g_min_len" />
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286 </when>
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287 <when value="-G" />
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288 </conditional>
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289
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290 <conditional name="polyx_tail_trimming">
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291 <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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292 <option value="" selected="true">Disable polyX trimming</option>
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293 <option value="-x">Enable polyX tail trimming</option>
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294 </param>
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295 <when value="-x">
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296 <param argument="--poly_x_min_len" type="integer" optional="true" label="PolyX minimum length"
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297 help="The minimum length to detect polyX in the read tail. 10 by default."/>
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298 </when>
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299 <when value="" />
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300 </conditional>
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301
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302 <section name="umi_processing" title="UMI processing" expanded="True">
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303 <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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304 <param argument="--umi_loc" type="text" optional="true" label="UMI location" help="Specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none."/>
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305 <param argument="--umi_len" type="integer" optional="true" label="UMI length" help="If the UMI is in read1/read2, its length should be provided."/>
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306 <param argument="--umi_prefix" type="text" optional="true" label="UMI prefix" help="If specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default."/>
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307 </section>
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308
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309 <section name="cutting_by_quality_options" title="Per read cutting by quality options" expanded="True">
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310 <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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311 <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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312 <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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313 <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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314 </section>
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315
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316 <section name="base_correction_options" title="Base correction by overlap analysis options" expanded="True">
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317 <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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318 </section>
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319 </section>
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320
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321 <section name="output_options" title="Output Options" expanded="False">
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322 <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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323 <param name="report_json" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Output JSON report" help="The JSON report contains all the data visualized in the HTML report. The format of the JSON report is manually optimized to be easily readable by humans and is compatible with MultiQC"/>
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324 </section>
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325 </inputs>
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326
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327 <outputs>
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328 <data name="out1" format_source="single_paired|in1" label="${tool.name} on ${on_string}: Read 1 output">
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329 <filter>single_paired['single_paired_selector'] == "single"</filter>
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330 </data>
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331 <collection name="output_paired_coll" type="paired" format_source="single_paired|paired_input['forward']" label="${tool.name} on ${on_string}: Paired-end output">
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332 <filter>single_paired['single_paired_selector'] == "paired_collection" and not single_paired['merge_reads']['merge']</filter>
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333 </collection>
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334
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335 <data name="report_html" format="html" from_work_dir="fastp.html" label="${tool.name} on ${on_string}: HTML report">
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336 <filter>output_options['report_html'] is True</filter>
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337 </data>
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338 <data name="report_json" format="json" from_work_dir="fastp.json" label="${tool.name} on ${on_string}: JSON report">
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339 <filter>output_options['report_json'] is True</filter>
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340 </data>
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341 <data name="merged_reads" format_source="single_paired|paired_input['forward']" label="${tool.name} on ${on_string}: Merged reads">
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342 <filter>single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge']</filter>
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343 </data>
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344 <collection name="unmerged_out_coll" type="paired" format_source="single_paired|paired_input['forward']" label="${tool.name} on ${on_string}: Unmerged filtered">
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345 <filter>single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
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346 </collection>
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347 <collection name="unpaired_out_coll" type="paired" format_source="single_paired|paired_input['forward']" label="${tool.name} on ${on_string}: Unmerged unfiltered">
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348 <filter>single_paired['single_paired_selector'] == "paired_collection" and single_paired['merge_reads']['merge'] and not single_paired['merge_reads']['include_unmerged']</filter>
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349 </collection>
0
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350 </outputs>
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351
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352 <tests>
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parents: 9
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353 <!-- 1. Ensure default output works -->
13
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parents: 12
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354 <test expect_num_outputs="3">
16
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parents: 15
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355 <conditional name="single_paired">
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356 <param name="single_paired_selector" value="single"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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357 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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358 </conditional>
1
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359 <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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parents: 0
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360 <output name="report_html">
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361 <assert_contents>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
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362 <has_text text="fastp report"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
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363 </assert_contents>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
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364 </output>
13
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iuc
parents: 12
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365 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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366 <assert_contents>
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iuc
parents: 12
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367 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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parents: 12
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368 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
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369 </output>
0
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370 </test>
11
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371 <!-- 2. Ensure paired collection works -->
7
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parents: 6
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372 <test expect_num_outputs="4">
16
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373 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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374 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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375 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
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376 <collection type="paired">
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377 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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378 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
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379 </collection>
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parents: 15
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380 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
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381 </conditional>
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iuc
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382 <section name="output_options">
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iuc
parents: 15
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383 <param name="report_json" value="False" />
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384 </section>
5
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parents: 4
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385 <output name="report_html">
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386 <assert_contents>
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iuc
parents: 4
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387 <has_text text="fastp report"/>
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iuc
parents: 4
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388 </assert_contents>
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parents: 4
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389 </output>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
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390 <output_collection name="output_paired_coll" type="paired">
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
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391 <element name="forward" value="out_bwa1.fq" ftype="fastqsanger"/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
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392 <element name="reverse" value="out_bwa2.fq" ftype="fastqsanger"/>
3e2551a37201 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit f3673fca1a180ada77fca93d871b3fd446f74498
iuc
parents: 4
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393 </output_collection>
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iuc
parents: 4
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394 </test>
11
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parents: 9
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395 <!-- 3. Ensure custom adapter works -->
1
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iuc
parents: 0
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396 <test expect_num_outputs="2">
16
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parents: 15
diff changeset
397 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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398 <param name="single_paired_selector" value="single"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
399 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
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400 <section name="adapter_trimming_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
401 <param name="adapter_sequence1" value="ATCG"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
diff changeset
402 </section>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
diff changeset
403 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
404 <section name="output_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
405 <param name="report_json" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
diff changeset
406 </section>
13
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parents: 12
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407 <output name="out1" ftype="fastqsanger" file="out_a.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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408 </test>
11
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parents: 9
diff changeset
409 <!-- 4. Ensure UMI processing works -->
1
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iuc
parents: 0
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410 <test expect_num_outputs="2">
16
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parents: 15
diff changeset
411 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
diff changeset
412 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
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413 <param name="single_paired_selector" value="single"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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414 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
diff changeset
415 <section name="read_mod_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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416 <section name="umi_processing">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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diff changeset
417 <param name="umi" value="true"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
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418 <param name="umi_loc" value="read1"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
419 <param name="umi_len" value="8"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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parents: 15
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420 </section>
0
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421 </section>
16
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parents: 15
diff changeset
422 <section name="output_options">
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parents: 15
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423 <param name="report_json" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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424 </section>
13
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iuc
parents: 12
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425 <output name="out1" ftype="fastqsanger" file="out2.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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426 </test>
11
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parents: 9
diff changeset
427 <!-- 5. Ensure UMI processing with different lengths works -->
1
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iuc
parents: 0
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428 <test expect_num_outputs="2">
16
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parents: 15
diff changeset
429 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
430 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
431 <param name="single_paired_selector" value="single"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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diff changeset
432 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
433 <section name="read_mod_options">
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iuc
parents: 15
diff changeset
434 <section name="umi_processing">
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iuc
parents: 15
diff changeset
435 <param name="umi" value="true"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
436 <param name="umi_loc" value="read1"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
437 <param name="umi_len" value="12"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
438 </section>
0
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diff changeset
439 </section>
16
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iuc
parents: 15
diff changeset
440 <section name="output_options">
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iuc
parents: 15
diff changeset
441 <param name="report_json" value="False" />
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442 </section>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
443 <output name="out1" ftype="fastqsanger" file="out3.fq"/>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
444 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
445 <!-- 6. Ensure paired-end UMI processing of Read 1 works -->
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
446 <test expect_num_outputs="4">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
447 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
448 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
449 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
450 <collection type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
451 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
452 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
453 </collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
454 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
455 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
456 <section name="read_mod_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
457 <section name="umi_processing">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
458 <param name="umi" value="true"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
459 <param name="umi_loc" value="read1"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
460 <param name="umi_len" value="8"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
461 </section>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
462 </section>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
463 <section name="output_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
464 <param name="report_json" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
465 </section>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
466 <output_collection name="output_paired_coll" type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
467 <element name="forward" value="out_bwa_umi_read1_1.fq" ftype="fastqsanger"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
468 <element name="reverse" value="out_bwa_umi_read1_2.fq" ftype="fastqsanger"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
469 </output_collection>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
470 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
471 <!-- 7. Ensure paired-end UMI processing of Read 2 works -->
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
472 <test expect_num_outputs="5">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
473 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
474 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
475 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
476 <collection type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
477 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
478 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
479 </collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
480 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
481 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
482 <section name="read_mod_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
483 <section name="umi_processing">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
484 <param name="umi" value="true"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
485 <param name="umi_loc" value="read2"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
486 <param name="umi_len" value="8"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
487 </section>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
488 </section>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
489 <output_collection name="output_paired_coll" type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
490 <element name="forward" value="out_bwa_umi_read2_1.fq" ftype="fastqsanger"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
491 <element name="reverse" value="out_bwa_umi_read2_2.fq" ftype="fastqsanger"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
492 </output_collection>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
493 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
494 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
495 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
496 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
497 </output>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
498 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
499 <!-- 8. Ensure JSON report output works -->
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
500 <test expect_num_outputs="2">
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
501 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
502 <param name="single_paired_selector" value="single"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
503 <param name="in1" ftype="fastqsanger" value="R1.fq"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
504 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
505 <section name="output_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
506 <param name="report_html" value="False"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
507 </section>
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
508 <output name="out1" ftype="fastqsanger" file="out1.fq"/>
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
iuc
parents: 0
diff changeset
509 <output name="report_json">
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
510 <assert_contents>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
511 <has_text text="fastp report"/>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
512 </assert_contents>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
513 </output>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
514 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
515 <!-- 9. Ensure polyG trimming works -->
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
516 <test expect_num_outputs="3">
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
517 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
518 <param name="single_paired_selector" value="single"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
519 <param name="in1" ftype="fastqsanger.gz" value="R1.fq.gz"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
520 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
521 <section name="read_mod_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
522 <conditional name="polyg_tail_trimming">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
523 <param name="trimming_select" value="-g"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
524 <param name="poly_g_min_len" value="10"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
525 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
526 </section>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
527 <output name="out1" ftype="fastqsanger.gz" decompress="true" file="out1.fq.gz"/>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
528 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
529 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
530 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
531 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
532 </output>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
533 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
534 <!-- 10. Ensure polyX trimming works -->
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
535 <test expect_num_outputs="3">
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
536 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
537 <param name="single_paired_selector" value="single"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
538 <param name="in1" ftype="fastqsanger.gz" value="R1.fq.gz"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
539 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
540 <section name="read_mod_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
541 <conditional name="polyg_tail_trimming">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
542 <param name="trimming_select" value="-G"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
543 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
544 <conditional name="polyx_tail_trimming">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
545 <param name="polyx_trimming_select" value="-x"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
546 <param name="poly_x_min_len" value="10"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
547 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
548 </section>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
549 <output name="out1" ftype="fastqsanger.gz" decompress="true" file="out1.fq.gz"/>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
550 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
551 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
552 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
553 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
554 </output>
6
a935cbdf1c0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 72f3e06941d063dffce10741fcebea38a536ee15
iuc
parents: 5
diff changeset
555 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
556 <!-- 11. Test fastqsanger files with different length -->
11
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
557 <test expect_exit_code="255" expect_failure="true">
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
558 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
559 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
560 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
561 <collection type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
562 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
563 <element name="reverse" value="bwa-mem-fastq2_too_long.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
564 </collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
565 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
566 </conditional>
11
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
iuc
parents: 9
diff changeset
567 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
568 <!-- 12. Test merge reads in combination with paired -->
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
569 <test expect_num_outputs="7">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
570 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
571 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
572 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
573 <collection type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
574 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
575 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
576 </collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
577 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
578 <conditional name="merge_reads">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
579 <param name="merge" value="--merge" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
580 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
581 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
582 <section name="output_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
583 <param name="report_json" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
584 <param name="report_html" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
585 </section>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
586 <output name="merged_reads" ftype="fastqsanger" file="bwa-mem-merged-reads.fastqsanger" />
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
587 <output_collection name="unmerged_out_coll" type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
588 <element name="forward" value="bwa-mem-unmerged-filtered-reads1.fastqsanger" ftype="fastqsanger"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
589 <element name="reverse" value="bwa-mem-unmerged-filtered-reads2.fastqsanger" ftype="fastqsanger"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
590 </output_collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
591 <output_collection name="unpaired_out_coll" type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
592 <element name="forward" value="bwa-mem-unmerged-unfiltered-reads1.fastqsanger" ftype="fastqsanger"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
593 <element name="reverse" ftype="fastqsanger">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
594 <assert_contents>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
595 <has_size size="0" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
596 </assert_contents>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
597 </element>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
598 </output_collection>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
599 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
600 <!-- 13. Test merge and include_unmerged in combination with paired collection -->
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
601 <test expect_num_outputs="2">
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
602 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
603 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
604 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
605 <collection type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
606 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
607 <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
608 </collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
609 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
610 <conditional name="merge_reads">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
611 <param name="merge" value="--merge" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
612 <param name="include_unmerged" value="true" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
613 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
614 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
615 <section name="output_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
616 <param name="report_html" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
617 </section>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
618 <output name="merged_reads" ftype="fastqsanger" file="bwa-mem-merged-read-include-unmerged.fastqsanger" />
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
619 <output name="report_json">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
620 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
621 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
622 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
623 </output>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
624 </test>
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
625 <!-- 14. Test merge reads in combination with paired -->
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
626 <test expect_num_outputs="7">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
627 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
628 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
629 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
630 <collection type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
631 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
632 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
633 </collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
634 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
635 <conditional name="merge_reads">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
636 <param name="merge" value="--merge" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
637 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
638 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
639 <section name="output_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
640 <param name="report_html" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
641 <param name="report_json" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
642 </section>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
643 <output name="merged_reads" ftype="fastqsanger.gz" decompress="true" file="bwa-mem-merged-reads.fastqsanger.gz" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
644 <output_collection name="unmerged_out_coll" type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
645 <element name="forward" value="bwa-mem-unmerged-filtered-reads1.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
646 <element name="reverse" value="bwa-mem-unmerged-filtered-reads2.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
647 </output_collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
648 <output_collection name="unpaired_out_coll" type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
649 <element name="forward" value="bwa-mem-unmerged-unfiltered-reads1.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
650 <element name="reverse" ftype="fastqsanger.gz">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
651 <assert_contents>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
652 <has_size size="0" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
653 </assert_contents>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
654 </element>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
655 </output_collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
656 </test>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
657 <!-- 15. Test merge and include_unmerged in combination with paired collection -->
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
658 <test expect_num_outputs="2">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
659 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
660 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
661 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
662 <collection type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
663 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
664 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
665 </collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
666 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
667 <conditional name="merge_reads">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
668 <param name="merge" value="--merge" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
669 <param name="include_unmerged" value="true" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
670 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
671 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
672 <section name="output_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
673 <param name="report_html" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
674 </section>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
675 <output name="merged_reads" ftype="fastqsanger.gz" decompress="true" file="bwa-mem-merged-read-include-unmerged.fastqsanger.gz" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
676 <output name="report_json">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
677 <assert_contents>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
678 <has_text text="fastp report"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
679 </assert_contents>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
680 </output>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
681 </test>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
682 <!--16. Test paired collection in combination with compressed input-->
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
683 <test expect_num_outputs="4">
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
684 <conditional name="single_paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
685 <param name="single_paired_selector" value="paired_collection"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
686 <param name="paired_input">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
687 <collection type="paired">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
688 <element name="forward" value="bwa-mem-fastq-paired-collection/input_forward.fastqsanger.gz" ftype="fastqsanger.gz" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
689 <element name="reverse" value="bwa-mem-fastq-paired-collection/input_reverse.fastqsanger.gz" ftype="fastqsanger.gz" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
690 </collection>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
691 </param>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
692 </conditional>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
693 <section name="output_options">
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
694 <param name="report_json" value="False" />
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
695 </section>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
696 <output name="report_html">
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
697 <assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
698 <has_text text="fastp report"/>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
699 </assert_contents>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
700 </output>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
701 <output_collection name="output_paired_coll" type="paired">
16
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
702 <element name="forward" value="bwa-mem-fastq-paired-collection/output_forward.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
iuc
parents: 15
diff changeset
703 <element name="reverse" value="bwa-mem-fastq-paired-collection/output_reverse.fastqsanger.gz" decompress="true" ftype="fastqsanger.gz"/>
13
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
704 </output_collection>
dbfc505896e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 78e6d7efcb74d3baa4e5611a7be4ad82b51bfe0d
iuc
parents: 12
diff changeset
705 </test>
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
706 </tests>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
707 <help><![CDATA[
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
708 .. class:: infomark
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
709
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
iuc
parents:
diff changeset
710 **What it does**
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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711
11
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712 fastp_ is a tool designed to provide fast all-in-one preprocessing for FASTQ files. This tool is developed in C++ with multithreading supported to
c59d48774d03 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 61d055a8abacf009e8afe2d72377e6769ad08f42
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713 afford high performance.
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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714
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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715 *Features*
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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716
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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717 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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718
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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719 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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720
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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721 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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722
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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723 4. Cut adapters. Adapter sequences can be automatically detected, which means you don't have to input the adapter sequences to trim them.
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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724
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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725 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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726
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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727 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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728
13
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729 7. Preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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730
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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731 8. Report JSON format result for further interpreting
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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732
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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733 9. Visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative)
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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734
13
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735 10. Split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limiting the lines of each split file (*Not enabled in this Galaxy tool*)
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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736
1
f44e93b4529c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 6918a14442b7ebc56950917d668356feefaaaa28
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737 11. Support long reads (data from PacBio / Nanopore devices)
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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738
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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739 -----
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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740
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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741 **Inputs**
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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742
15
a626e8c0e1ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 17a0a67dfbc7541a7fe3618cfbbb71d814042889
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743 Single-end or Paired-end (compressed) fastqsanger files
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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744
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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745 -----
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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746
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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747 **Outputs**
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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748
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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749 * Processed reads
13
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750 * Merged reads
16
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751 * Unmerged filtered reads, reads that cannot be merged successfully, but both pass all the filters.
10678d49d39e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 81e2b45f5357c7ba235f219828a6998f146012c4
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752 * Unmerged unfiltered reads, reads that cannot be merged, i.e. **forward** passes filters but **reverse** doesn't.
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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753
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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754 Optionally, under **Output Options** you can choose to output
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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755
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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756 * HTML report (default is Yes)
4
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parents: 3
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757 * JSON report (compatible with MultiQC)
0
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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758
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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759 .. _fastp: https://github.com/OpenGene/fastp
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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760
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761 ]]></help>
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762 <citations>
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763 <citation type="doi">10.1101/274100</citation>
988729b728f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp commit 2e41f5d3dd8201a5f8295ec30095c508250a8304
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764 </citations>
16
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765 </tool>