Mercurial > repos > petr-novak > re_utils
annotate single_fastq_filtering.xml @ 24:b50db133106a draft
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author | petr-novak |
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date | Wed, 02 Aug 2023 12:28:39 +0000 |
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1 <tool id="single_fastq_filtering" name="Preprocessing of FASTQ 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 FASTQ read files |
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7 including trimming, quality filtering, cutadapt filtering and sampling |
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8 </description> |
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9 <requirements> |
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10 <requirement type="package">blast</requirement> |
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11 <requirement type="package">cutadapt</requirement> |
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12 <requirement type="package">bioconductor-shortread</requirement> |
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13 <requirement type="package">r-optparse</requirement> |
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14 </requirements> |
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15 <required_files> |
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16 <include type="literal" path="single_fastq_filtering_wrapper.sh"/> |
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17 <include type="literal" path="single_fastq_filtering.R"/> |
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18 </required_files> |
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19 <command interpreter="bash"> |
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20 bash '$__tool_directory__'/single_fastq_filtering_wrapper.sh -a ${A} -o ${output} |
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21 -c ${cut_off} -p ${percent_above} -N ${max_n} -G ${png_output} |
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23 #if $sampling.sequence_sampling : |
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24 -n $sampling.sample_size |
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25 #end if |
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27 #if $trimming.sequence_trimming : |
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28 -e $trimming.trim_end -s $trimming.trim_start |
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29 #end if |
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31 #if $cutadapt.use_custom : |
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32 -C "${cutadapt.custom_options}" |
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33 #end if |
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35 #if $similarity_filtering.include : |
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36 -F "${similarity_filtering.filter_database}" |
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37 #end if |
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39 | |
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40 </command> |
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42 <inputs> |
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43 <param format="fastq,fastq.gz" type="data" name="A" |
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44 label="Reads in FASTQ format"/> |
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45 <conditional name="sampling"> |
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46 <param name="sequence_sampling" type="boolean" truevalue="true" |
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47 falsevalue="false" checked="False" label="Read sampling"/> |
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48 <when value="false"> |
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49 <!-- do nothing here --> |
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50 </when> |
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51 <when value="true"> |
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52 <param name="sample_size" type="integer" |
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53 label="Sample size (number of reads)" |
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54 help="How many reads should be sampled" value="500000" min="0"/> |
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55 </when> |
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56 </conditional> |
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58 <param type="integer" name="cut_off" label="Quality cutoff" value="10" min="0" |
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59 help="See below how to correctly set the quality cutoff"/> |
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60 <param type="integer" name="percent_above" label="Percent above cutoff" value="95" |
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61 min="0" |
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62 help="Percentage of bases in the read that must have quality equal to or higher than the cutoff value"/> |
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64 <conditional name="trimming"> |
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65 <param name="sequence_trimming" type="boolean" truevalue="true" |
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66 falsevalue="false" checked="False" label="Trim reads"/> |
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67 <when value="false"> |
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68 <!-- do nothing here --> |
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69 </when> |
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70 <when value="true"> |
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71 <param type="integer" name="trim_start" label="Start position" value="1" |
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72 min="1" |
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73 help="Reads are trimmed at the specified start"/> |
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74 <param type="integer" name="trim_end" label="End position" value="100" |
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75 min="1" |
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76 help="Reads are trimmed to the specified end position, shorted sequences are discarded"/> |
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77 </when> |
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79 </conditional> |
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80 <param name="max_n" type="integer" label="maximum Ns" |
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81 help="Maximal number of Ns allowed in reads" value="0" min="0" max="10"/> |
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83 <conditional name="cutadapt"> |
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84 <param name="use_custom" type="boolean" truevalue="true" falsevalue="false" |
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85 checked="False" label="Custom cutadapt options"/> |
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86 <when value="false"> |
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87 <!-- do nothing here --> |
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88 </when> |
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89 <when value="true"> |
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90 <param name="custom_options" type="text" area="True" size="8x30" |
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91 label="Custom options" help="Consult cutadapt for usage" value=""> |
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92 <sanitizer sanitize="False"/> |
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93 </param> |
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94 > |
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95 </when> |
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96 </conditional> |
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98 <conditional name="similarity_filtering"> |
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99 <param name="include" type="boolean" truevalue="true" falsevalue="false" |
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100 checked="False" label="Use similarity search filtering"/> |
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101 <when value="false"> |
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102 <!-- do nothing here --> |
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103 </when> |
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104 <when value="true"> |
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106 <param name="filter_database" format="fasta" type="data" |
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107 label="Sequence filter database" |
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108 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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109 </when> |
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110 </conditional> |
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112 </inputs> |
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114 | |
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115 <outputs> |
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116 <data format="fasta" name="output" |
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117 label="Filtered FASTA reads from datasets ${A.hid}"/> |
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118 <data format="png" name="png_output" |
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119 label="Nucleotide composition after filtering of ${A.hid}"/>" |
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120 </outputs> |
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122 <tests> |
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123 <test> |
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124 <param name="A" value="ERR215189_1_part.fastq.gz"/> |
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125 <param name="max_n" value="0"/> |
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126 <param name="cut_off" value="10"/> |
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127 <param name="percent_above" value="95"/> |
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128 <output name="output" value="single_output.fasta"/> |
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129 <output name="png_output" value="single_output.png"/> |
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130 </test> |
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131 </tests> |
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133 <help> |
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134 **What it does** |
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136 This tool is designed to perform preprocessing of fastq file. Input files can be |
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137 in GNU zipped archive (.gz extension). Reads are filtered based on the quality, |
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138 presence of N bases and adapters. All reads which pass the quality filter fill |
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139 be writen into output files. If sampling is specified, only sample of sequences |
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140 will be returned. |
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142 Cutadapt us run with this options:: |
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144 --anywhere='AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' |
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145 --anywhere='AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' |
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146 --anywhere='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' |
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147 --anywhere='ATCTCGTATGCCGTCTTCTGCTTG' |
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148 --anywhere='CAAGCAGAAGACGGCATACGAGAT' |
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149 --anywhere='GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC' |
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150 --error-rate=0.05 |
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151 --times=1 --overlap=15 --discard |
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153 | |
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154 **Order of fastq files processing** |
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156 1. Trimming (optional) |
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157 #. Filter by quality |
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158 #. Cutadapt filtering |
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159 #. Sampling (optional) |
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160 #. Interlacing two fasta files |
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162 **Quality setting cutoff** |
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164 To correctly set quality cutoff, you need to know how the quality is encoded in |
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165 your fastq file, default |
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166 filtering which is suitable for Sanger and Illumina 1.8 encoding is shown below:: |
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168 | |
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169 Default filtering cutoff |
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170 | |
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171 | |
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172 V |
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173 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS..................................................... |
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174 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................... |
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175 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII...................... |
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176 .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ...................... |
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177 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL.................................................... |
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178 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ |
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179 | | | | | | |
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180 33 59 64 73 104 126 |
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181 0........................26...31.......40 |
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182 -5....0........9.............................40 |
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183 0........9.............................40 |
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184 3.....9.............................40 |
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185 0.2......................26...31........41 |
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186 |
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187 S - Sanger Phred+33, raw reads typically (0, 40) |
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188 X - Solexa Solexa+64, raw reads typically (-5, 40) |
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189 I - Illumina 1.3+ Phred+64, raw reads typically (0, 40) |
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190 J - Illumina 1.5+ Phred+64, raw reads typically (3, 40) |
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191 with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) |
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192 (Note: See discussion above). |
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193 L - Illumina 1.8+ Phred+33, raw reads typically (0, 41) |
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194 |
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195 </help> |
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197 |