Mercurial > repos > petr-novak > re_utils
annotate paired_fastq_filtering.xml @ 28:ba970b24e48c draft
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author | petr-novak |
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date | Wed, 02 Aug 2023 13:09:47 +0000 |
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1 <tool id="paired_fastq_filtering" name="Preprocessing of FASTQ paired-end reads" version="1.0.0.3"> |
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2 <stdio> |
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3 <exit_code range="1:" level="fatal" description="Error"/> |
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4 </stdio> |
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5 <description> |
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6 Preprocessing of paired-end reads in FASTQ format |
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7 including trimming, quality filtering, cutadapt filtering and interlacing. Broken |
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8 pairs are discarded. |
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9 </description> |
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10 <requirements> |
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11 <requirement type="package">blast</requirement> |
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12 <requirement type="package">cutadapt</requirement> |
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13 <requirement type="package">bioconductor-shortread</requirement> |
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14 <requirement type="package">r-optparse</requirement> |
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15 </requirements> |
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16 <required_files> |
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17 <include type="literal" path="paired_fastq_filtering_wrapper.sh"/> |
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18 <include type="literal" path="paired_fastq_filtering.R"/> |
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19 <include type="literal" path="fasta_interlacer.py"/> |
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20 </required_files> |
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21 <command> |
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22 bash '$__tool_directory__'/paired_fastq_filtering_wrapper.sh -a ${A} -b ${B} -o |
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23 ${paired} -c ${cut_off} -p ${percent_above} -N ${max_n} $rename -G ${png_output} |
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25 #if $sampling.sequence_sampling : |
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26 -n $sampling.sample_size |
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27 #end if |
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29 #if $trimming.sequence_trimming : |
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30 -e $trimming.trim_end -s $trimming.trim_start |
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31 #end if |
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33 #if $cutadapt.use_custom : |
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34 -C "${cutadapt.custom_options}" |
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35 #end if |
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37 #if $similarity_filtering.include : |
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38 -F "${similarity_filtering.filter_database}" |
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39 #end if |
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41 </command> |
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43 <inputs> |
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44 <param format="fastq,fastq.gz" type="data" name="A" label="Left-hand reads"/> |
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46 <param format="fastq,fastq.gz" type="data" name="B" label="Right-hand reads"/> |
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48 <conditional name="sampling"> |
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49 <param name="sequence_sampling" type="boolean" truevalue="true" |
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50 falsevalue="false" checked="False" label="Read sampling"/> |
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51 <when value="false"> |
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52 <!-- do nothing here --> |
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53 </when> |
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54 <when value="true"> |
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55 <param name="sample_size" type="integer" |
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56 label="Sample size (number of pairs)" |
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57 help="How many read pairs should be sampled" value="500000" |
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58 min="0"/> |
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59 </when> |
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60 </conditional> |
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62 <param type="integer" name="cut_off" label="Quality cutoff" value="10" min="0" |
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63 help="See below how to correctly set the quality cutoff"/> |
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64 <param type="integer" name="percent_above" label="Percent above cutoff" value="95" |
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65 min="0" |
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66 help="Percentage of bases in the read that must have quality equal to or higher than the cutoff value"/> |
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68 <conditional name="trimming"> |
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69 <param name="sequence_trimming" type="boolean" truevalue="true" |
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70 falsevalue="false" checked="False" label="Trim reads"/> |
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71 <when value="false"> |
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72 <!-- do nothing here --> |
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73 </when> |
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74 <when value="true"> |
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75 <param type="integer" name="trim_start" label="Start position" value="1" |
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76 min="1" |
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77 help="Reads are trimmed at the specified start"/> |
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78 <param type="integer" name="trim_end" label="End position" value="100" |
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79 min="1" |
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80 help="Reads are trimmed to the specified end position, shorted sequences are discarded"/> |
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81 </when> |
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83 </conditional> |
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84 <param name="max_n" type="integer" label="Maximum Ns" |
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85 help="Maximal number of Ns allowed in reads" value="0" min="0" max="10"/> |
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86 |
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87 <conditional name="cutadapt"> |
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88 <param name="use_custom" type="boolean" truevalue="true" falsevalue="false" |
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89 checked="False" label="Custom cutadapt options"/> |
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90 <when value="false"> |
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91 <!-- do nothing here --> |
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92 </when> |
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93 <when value="true"> |
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94 <param name="custom_options" type="text" area="True" size="8x30" |
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95 label="Custom options" help="Consult cutadapt for usage" value=""> |
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96 <sanitizer sanitize="False"/> |
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97 </param> |
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98 > |
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99 </when> |
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100 </conditional> |
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102 <conditional name="similarity_filtering"> |
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103 <param name="include" type="boolean" truevalue="true" falsevalue="false" |
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104 checked="False" label="Use similarity search filtering"/> |
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105 <when value="false"> |
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106 <!-- do nothing here --> |
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107 </when> |
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108 <when value="true"> |
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110 <param name="filter_database" format="fasta" type="data" |
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111 label="Sequence filter database" |
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112 help="Provide DNA sequences in FASTA format. Reads that have at least 90% similarity over 90% of their length to sequence in the filter database will be removed. This option is suitable for removing organellar or other contaminating sequences."/> |
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113 </when> |
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114 </conditional> |
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116 <param name="rename" type="boolean" truevalue="-R" falsevalue="" checked="True" |
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117 label="Rename reads" |
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118 help="By default, original read names are used. In case your reads do not follow proper naming scheme to label paired-end mates, use this option. All read pairs must be complete!"/> |
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119 </inputs> |
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121 | |
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122 <outputs> |
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123 <data format="fasta" name="paired" |
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124 label="Interlaced paired reads from datasets ${A.hid} and ${B.hid} "/> |
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125 <data format="png" name="png_output" |
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126 label="Nucleotide composition after filtering of ${A.hid} and ${B.hid} "/>" |
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127 </outputs> |
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129 | |
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130 <tests> |
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131 <test> |
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132 <param name="A" value="ERR215189_1_part.fastq.gz"/> |
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133 <param name="B" value="ERR215189_2_part.fastq.gz"/> |
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134 <param name="max_n" value="0"/> |
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135 <param name="cut_off" value="10"/> |
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136 <param name="percent_above" value="95"/> |
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137 <output name="output" value="paired_output.fasta"/> |
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138 <output name="png_output" value="paired_output.png"/> |
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139 </test> |
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140 </tests> |
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142 <help> |
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143 **What it does** |
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145 This tool is designed to make memory efficient preprocessing of two |
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146 fastq files. Output of this file can be used as input of RepeatExplorer |
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147 clustering. |
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148 Input files can be in GNU zipped archive (.gz extension). |
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149 Reads are filtered based on the quality, presence of N bases and |
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150 adapters. Two input fastq files are procesed in parallel. Only complete pair |
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151 are kept. As the input files are process in chunks, it is required that |
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152 pair reads are complete and in the same order in both input files. All |
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153 reads which pass the quality filter fill be writen into output files. |
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154 If sampling is specified, only sample of sequences will be |
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155 returned. Cutadapt us run with this options:: |
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157 --anywhere='AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' |
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158 --anywhere='AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' |
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159 --anywhere='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' |
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160 --anywhere='ATCTCGTATGCCGTCTTCTGCTTG' |
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161 --anywhere='CAAGCAGAAGACGGCATACGAGAT' |
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162 --anywhere='GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC' |
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163 --error-rate=0.05 |
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164 --times=1 --overlap=15 --discard |
0 | 165 |
166 | |
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167 **Order of fastq files processing** |
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169 1. Trimming (optional) |
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170 #. Filter by quality |
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171 #. Discard single reads, keep complete pairs |
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172 #. Cutadapt filtering |
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173 #. Discard single reads, keep complete pairs |
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174 #. Sampling (optional) |
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175 #. Interlacing two fasta files |
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177 **Quality setting cutoff** |
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179 To correctly set quality cutoff, you need to know how the quality is encoded in |
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180 your fastq file, default |
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181 filtering which is suitable for Sanger and Illumina 1.8 encoding is shown below:: |
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183 | |
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184 Default filtering cutoff |
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185 | |
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186 | |
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187 V |
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188 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS..................................................... |
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189 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................... |
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190 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII...................... |
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191 .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ...................... |
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192 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL.................................................... |
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193 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ |
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194 | | | | | | |
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195 33 59 64 73 104 126 |
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196 0........................26...31.......40 |
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197 -5....0........9.............................40 |
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198 0........9.............................40 |
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199 3.....9.............................40 |
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200 0.2......................26...31........41 |
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201 |
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202 S - Sanger Phred+33, raw reads typically (0, 40) |
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203 X - Solexa Solexa+64, raw reads typically (-5, 40) |
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204 I - Illumina 1.3+ Phred+64, raw reads typically (0, 40) |
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205 J - Illumina 1.5+ Phred+64, raw reads typically (3, 40) |
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206 with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) |
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207 (Note: See discussion above). |
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208 L - Illumina 1.8+ Phred+33, raw reads typically (0, 41) |
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209 |
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210 </help> |
0 | 211 </tool> |
212 |