Mercurial > repos > petr-novak > re_utils
comparison single_fastq_filtering.xml @ 0:a4cd8608ef6b draft
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author | petr-novak |
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date | Mon, 01 Apr 2019 07:56:36 -0400 |
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children | 378565f5a875 |
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1 <tool id="single_fastq_filtering" name="Preprocessing of fastq reads"> | |
2 <description> | |
3 Preprocessing of fastq files | |
4 including trimming, quality filtering, cutadapt filtering and sampling | |
5 </description> | |
6 <requirements> | |
7 <requirement type="package">blast</requirement> | |
8 <requirement type="package">cutadapt</requirement> | |
9 <requirement type="package">bioconductor-shortread</requirement> | |
10 <requirement type="package">r-optparse</requirement> | |
11 </requirements> | |
12 <command interpreter="bash"> | |
13 single_fastq_filtering_wrapper.sh -a ${A} -o ${output} -c ${cut_off} -p ${percent_above} -N ${max_n} -G ${png_output} | |
14 | |
15 #if $sampling.sequence_sampling : | |
16 -n $sampling.sample_size | |
17 #end if | |
18 | |
19 #if $trimming.sequence_trimming : | |
20 -e $trimming.trim_end -s $trimming.trim_start | |
21 #end if | |
22 | |
23 #if $cutadapt.use_custom : | |
24 -C "${cutadapt.custom_options}" | |
25 #end if | |
26 | |
27 #if $similarity_filtering.include : | |
28 -F "${similarity_filtering.filter_database}" | |
29 #end if | |
30 | |
31 | |
32 </command> | |
33 | |
34 <inputs> | |
35 <param format="fastq,fastq.gz" type="data" name="A" label="reads in fastq format" /> | |
36 <conditional name="sampling"> | |
37 <param name="sequence_sampling" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sequence sampling"/> | |
38 <when value="false"> | |
39 <!-- do nothing here --> | |
40 </when> | |
41 <when value="true"> | |
42 <param name="sample_size" type="integer" label="Sample size(number of reads" help="How many sequence reads should be in resulting dataset" value="500000" min="0"/> | |
43 </when> | |
44 </conditional> | |
45 | |
46 <param type="integer" name="cut_off" label="Quality cut-off" value="10" min="0" help="see below how to correctly set quality cut-off" /> | |
47 <param type="integer" name="percent_above" label="percent above cutoff" value="95" min="0" | |
48 help="Percent of bases in sequence that must have quality equal to / higher than cut-off value" /> | |
49 | |
50 <conditional name="trimming"> | |
51 <param name="sequence_trimming" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Trim sequences"/> | |
52 <when value="false"> | |
53 <!-- do nothing here --> | |
54 </when> | |
55 <when value="true"> | |
56 <param type="integer" name="trim_start" label="trimming - start position" value="1" min="1" | |
57 help="sequences are trimmed at specified start" /> | |
58 <param type="integer" name="trim_end" label="trimming - end position" value="100" min="1" | |
59 help="sequences are trimmed to specified end position, shorted sequences are discarded" /> | |
60 </when> | |
61 | |
62 </conditional> | |
63 <param name="max_n" type="integer" label="maximum Ns" help="Maximum number of Ns in sequence" value="0" min="0" max="10"/> | |
64 | |
65 <conditional name="cutadapt"> | |
66 <param name="use_custom" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Do you want to use custom cutadapt options"/> | |
67 <when value="false"> | |
68 <!-- do nothing here --> | |
69 </when> | |
70 <when value="true"> | |
71 <param name="custom_options" type="text" area="True" size="8x30" label="Cutadapt custom options" help="Consult cutadapt for usage" value=""> | |
72 <sanitizer sanitize="False"/> | |
73 </param>> | |
74 </when> | |
75 </conditional> | |
76 | |
77 <conditional name="similarity_filtering"> | |
78 <param name="include" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Use similarity search filtering"/> | |
79 <when value="false"> | |
80 <!-- do nothing here --> | |
81 </when> | |
82 <when value="true"> | |
83 | |
84 <param name="filter_database" format="fasta" type="data" label="Sequence filter database" help="Provide DNA sequences in fasta format. Sequence reads which has at least 90% similarity over 90% of length to sequence in filter database will be removed. This is suitable option if you want to remove organele DNA or contamination"/> | |
85 </when> | |
86 </conditional> | |
87 | |
88 </inputs> | |
89 | |
90 | |
91 <outputs> | |
92 <data format="fasta" name="output" label="filtered fasta reads from datasets ${A.hid}"/> | |
93 <data format="png" name="png_output" label="nucleotide composition after filtering of ${A.hid}"/>" | |
94 </outputs> | |
95 | |
96 <tests> | |
97 <test> | |
98 <param name="A" value="ERR215189_1_part.fastq.gz" /> | |
99 <param name="max_n" value="0"/> | |
100 <param name="cut_off" value="10" /> | |
101 <param name="percent_above" value="95" /> | |
102 <output name="output" value="single_output.fasta" /> | |
103 <output name="png_output" value="single_output.png" /> | |
104 </test> | |
105 </tests> | |
106 | |
107 <help> | |
108 **What it does** | |
109 | |
110 This tool is designed to perform preprocessing of fastq file. Input files can be | |
111 in GNU zipped archive (.gz extension). Reads are filtered based on the quality, | |
112 presence of N bases and adapters. All reads which pass the quality filter fill | |
113 be writen into output files. If sampling is specified, only sample of sequences | |
114 will be returned. | |
115 | |
116 Cutadapt us run with this options:: | |
117 | |
118 --anywhere='AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' | |
119 --anywhere='AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' | |
120 --anywhere='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' | |
121 --anywhere='ATCTCGTATGCCGTCTTCTGCTTG' | |
122 --anywhere='CAAGCAGAAGACGGCATACGAGAT' | |
123 --anywhere='GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC' | |
124 --error-rate=0.05 | |
125 --times=1 --overlap=15 --discard | |
126 | |
127 | |
128 **Order of fastq files processing** | |
129 | |
130 1. Trimming (optional) | |
131 #. Filter by quality | |
132 #. Cutadapt filtering | |
133 #. Sampling (optional) | |
134 #. Interlacing two fasta files | |
135 | |
136 **Quality setting cut-off** | |
137 | |
138 To correctly set quality cut-off, you need to know how the quality is encoded in your fastq file, default | |
139 filtering which is suitable for Sanger and Illumina 1.8 encoding is shown below:: | |
140 | |
141 | |
142 Default filtering cut-off | |
143 | | |
144 | | |
145 V | |
146 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS..................................................... | |
147 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................... | |
148 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII...................... | |
149 .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ...................... | |
150 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL.................................................... | |
151 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ | |
152 | | | | | | | |
153 33 59 64 73 104 126 | |
154 0........................26...31.......40 | |
155 -5....0........9.............................40 | |
156 0........9.............................40 | |
157 3.....9.............................40 | |
158 0.2......................26...31........41 | |
159 | |
160 S - Sanger Phred+33, raw reads typically (0, 40) | |
161 X - Solexa Solexa+64, raw reads typically (-5, 40) | |
162 I - Illumina 1.3+ Phred+64, raw reads typically (0, 40) | |
163 J - Illumina 1.5+ Phred+64, raw reads typically (3, 40) | |
164 with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) | |
165 (Note: See discussion above). | |
166 L - Illumina 1.8+ Phred+33, raw reads typically (0, 41) | |
167 | |
168 </help> | |
169 </tool> | |
170 |