Mercurial > repos > petr-novak > re_utils
annotate single_fastq_filtering.xml @ 34:91996b991991 draft default tip
Uploaded
author | petr-novak |
---|---|
date | Fri, 16 Feb 2024 15:22:21 +0000 |
parents | f1738f8649b0 |
children |
rev | line source |
---|---|
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
1 <tool id="single_fastq_filtering" name="Preprocessing of FASTQ reads" version="1.0.0.3"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
2 <stdio> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
3 <exit_code range="1:" level="fatal" description="Error"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
4 </stdio> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
5 <description> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
6 Preprocessing of FASTQ read files |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
7 including trimming, quality filtering, cutadapt filtering and sampling |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
8 </description> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
9 <requirements> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
10 <requirement type="package">blast</requirement> |
33
f1738f8649b0
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
petr-novak
parents:
22
diff
changeset
|
11 <requirement type="package" version="4.4">cutadapt</requirement> |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
12 <requirement type="package">bioconductor-shortread</requirement> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
13 <requirement type="package">r-optparse</requirement> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
14 </requirements> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
15 <required_files> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
16 <include type="literal" path="single_fastq_filtering_wrapper.sh"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
17 <include type="literal" path="single_fastq_filtering.R"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
18 </required_files> |
33
f1738f8649b0
planemo upload commit 39094a128ea3dd2c39f4997c6de739c33c07e5f3-dirty
petr-novak
parents:
22
diff
changeset
|
19 <command> |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
20 bash '$__tool_directory__'/single_fastq_filtering_wrapper.sh -a ${A} -o ${output} |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
21 -c ${cut_off} -p ${percent_above} -N ${max_n} -G ${png_output} |
0 | 22 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
23 #if $sampling.sequence_sampling : |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
24 -n $sampling.sample_size |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
25 #end if |
0 | 26 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
27 #if $trimming.sequence_trimming : |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
28 -e $trimming.trim_end -s $trimming.trim_start |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
29 #end if |
0 | 30 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
31 #if $cutadapt.use_custom : |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
32 -C "${cutadapt.custom_options}" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
33 #end if |
0 | 34 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
35 #if $similarity_filtering.include : |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
36 -F "${similarity_filtering.filter_database}" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
37 #end if |
0 | 38 |
39 | |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
40 </command> |
0 | 41 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
42 <inputs> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
43 <param format="fastq,fastq.gz" type="data" name="A" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
44 label="Reads in FASTQ format"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
45 <conditional name="sampling"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
46 <param name="sequence_sampling" type="boolean" truevalue="true" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
47 falsevalue="false" checked="False" label="Read sampling"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
48 <when value="false"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
49 <!-- do nothing here --> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
50 </when> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
51 <when value="true"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
52 <param name="sample_size" type="integer" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
53 label="Sample size (number of reads)" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
54 help="How many reads should be sampled" value="500000" min="0"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
55 </when> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
56 </conditional> |
0 | 57 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
58 <param type="integer" name="cut_off" label="Quality cutoff" value="10" min="0" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
59 help="See below how to correctly set the quality cutoff"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
60 <param type="integer" name="percent_above" label="Percent above cutoff" value="95" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
61 min="0" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
62 help="Percentage of bases in the read that must have quality equal to or higher than the cutoff value"/> |
0 | 63 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
64 <conditional name="trimming"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
65 <param name="sequence_trimming" type="boolean" truevalue="true" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
66 falsevalue="false" checked="False" label="Trim reads"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
67 <when value="false"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
68 <!-- do nothing here --> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
69 </when> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
70 <when value="true"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
71 <param type="integer" name="trim_start" label="Start position" value="1" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
72 min="1" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
73 help="Reads are trimmed at the specified start"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
74 <param type="integer" name="trim_end" label="End position" value="100" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
75 min="1" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
76 help="Reads are trimmed to the specified end position, shorted sequences are discarded"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
77 </when> |
0 | 78 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
79 </conditional> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
80 <param name="max_n" type="integer" label="maximum Ns" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
81 help="Maximal number of Ns allowed in reads" value="0" min="0" max="10"/> |
0 | 82 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
83 <conditional name="cutadapt"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
84 <param name="use_custom" type="boolean" truevalue="true" falsevalue="false" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
85 checked="False" label="Custom cutadapt options"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
86 <when value="false"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
87 <!-- do nothing here --> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
88 </when> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
89 <when value="true"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
90 <param name="custom_options" type="text" area="True" size="8x30" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
91 label="Custom options" help="Consult cutadapt for usage" value=""> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
92 <sanitizer sanitize="False"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
93 </param> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
94 > |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
95 </when> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
96 </conditional> |
0 | 97 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
98 <conditional name="similarity_filtering"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
99 <param name="include" type="boolean" truevalue="true" falsevalue="false" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
100 checked="False" label="Use similarity search filtering"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
101 <when value="false"> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
102 <!-- do nothing here --> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
103 </when> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
104 <when value="true"> |
0 | 105 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
106 <param name="filter_database" format="fasta" type="data" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
107 label="Sequence filter database" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
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."/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
109 </when> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
110 </conditional> |
0 | 111 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
112 </inputs> |
0 | 113 |
114 | |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
115 <outputs> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
116 <data format="fasta" name="output" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
117 label="Filtered FASTA reads from datasets ${A.hid}"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
118 <data format="png" name="png_output" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
119 label="Nucleotide composition after filtering of ${A.hid}"/>" |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
120 </outputs> |
0 | 121 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
122 <tests> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
123 <test> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
124 <param name="A" value="ERR215189_1_part.fastq.gz"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
125 <param name="max_n" value="0"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
126 <param name="cut_off" value="10"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
127 <param name="percent_above" value="95"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
128 <output name="output" value="single_output.fasta"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
129 <output name="png_output" value="single_output.png"/> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
130 </test> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
131 </tests> |
0 | 132 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
133 <help> |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
134 **What it does** |
0 | 135 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
136 This tool is designed to perform preprocessing of fastq file. Input files can be |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
137 in GNU zipped archive (.gz extension). Reads are filtered based on the quality, |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
138 presence of N bases and adapters. All reads which pass the quality filter fill |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
139 be writen into output files. If sampling is specified, only sample of sequences |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
140 will be returned. |
0 | 141 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
142 Cutadapt us run with this options:: |
0 | 143 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
144 --anywhere='AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT' |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
145 --anywhere='AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
146 --anywhere='GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
147 --anywhere='ATCTCGTATGCCGTCTTCTGCTTG' |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
148 --anywhere='CAAGCAGAAGACGGCATACGAGAT' |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
149 --anywhere='GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC' |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
150 --error-rate=0.05 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
151 --times=1 --overlap=15 --discard |
0 | 152 |
153 | |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
154 **Order of fastq files processing** |
0 | 155 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
156 1. Trimming (optional) |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
157 #. Filter by quality |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
158 #. Cutadapt filtering |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
159 #. Sampling (optional) |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
160 #. Interlacing two fasta files |
0 | 161 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
162 **Quality setting cutoff** |
0 | 163 |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
164 To correctly set quality cutoff, you need to know how the quality is encoded in |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
165 your fastq file, default |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
166 filtering which is suitable for Sanger and Illumina 1.8 encoding is shown below:: |
0 | 167 |
168 | |
22
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
169 Default filtering cutoff |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
170 | |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
171 | |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
172 V |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
173 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS..................................................... |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
174 ..........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...................... |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
175 ...............................IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII...................... |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
176 .................................JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ...................... |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
177 LLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL.................................................... |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
178 !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
179 | | | | | | |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
180 33 59 64 73 104 126 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
181 0........................26...31.......40 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
182 -5....0........9.............................40 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
183 0........9.............................40 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
184 3.....9.............................40 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
185 0.2......................26...31........41 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
186 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
187 S - Sanger Phred+33, raw reads typically (0, 40) |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
188 X - Solexa Solexa+64, raw reads typically (-5, 40) |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
189 I - Illumina 1.3+ Phred+64, raw reads typically (0, 40) |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
190 J - Illumina 1.5+ Phred+64, raw reads typically (3, 40) |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
191 with 0=unused, 1=unused, 2=Read Segment Quality Control Indicator (bold) |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
192 (Note: See discussion above). |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
193 L - Illumina 1.8+ Phred+33, raw reads typically (0, 41) |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
194 |
58807b35777a
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
petr-novak
parents:
10
diff
changeset
|
195 </help> |
0 | 196 </tool> |
197 |