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comparison fastq_masker.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fastq_masker" name="Mask nucleotides">
2 <description>(based on quality)</description>
3 <command>
4 cat '$input' |
5 fastq_masker
6 #if $input.ext == "fastqsanger":
7 -Q 33
8 #elif $input.ext == "fastq":
9 -Q 64
10 #end if
11 -v -q $cutoff -r '$maskchar' -o '$output'</command>
12 <inputs>
13 <param format="fastq,fastqsanger" name="input" type="data" label="Library to clip" />
14
15 <param name="cutoff" size="4" type="integer" value="20">
16 <label>Minimum quality score</label>
17 <help>Nucleotides below this quality will be masked</help>
18 </param>
19
20 <param name="maskchar" size="1" type="text" value="N">
21 <label>Mask character</label>
22 <help>Replace low-quality nucleotides with this character. Common values: 'N' or '.'</help>
23 </param>
24 </inputs>
25
26 <tests>
27 <test>
28 <param name="input" value="fastq_masker.fastq" ftype="fastq" />
29 <param name="cutoff" value="29"/>
30 <param name="maskchar" value="x"/>
31 <output name="output" file="fastq_masker.out" />
32 </test>
33 </tests>
34
35 <outputs>
36 <data format="input" name="output" metadata_source="input"
37 />
38 </outputs>
39 <help>
40 **What it does**
41
42 This tool masks low-quality nucleotides in a FASTQ file, and replaces them with the specifed mask character (**N** by default).
43
44 --------
45
46 **Example**
47
48 Input FASTQ file::
49
50 @1
51 TATGGTCAGAAACCATATGC
52 +1
53 40 40 40 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19
54 @2
55 CAGCGAGGCTTTAATGCCAT
56 +2
57 40 40 40 40 40 40 40 40 30 20 19 20 19 19 19 19 19 19 19 19
58 @3
59 CAGCGAGGCTTTAATGCCAT
60 +3
61 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 19 19 19
62
63 After Masking nucleotides with quality lower than 20 with the character **N**::
64
65 @1
66 TATGGTCAGAAANNNNNNNN
67 +1
68 40 40 40 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19
69 @2
70 CAGCGAGGCTNTNNNNNNNN
71 +2
72 40 40 40 40 40 40 40 40 30 20 19 20 19 19 19 19 19 19 19 19
73 @3
74 CAGCGAGGCNNNNNNNNNNN
75 +3
76 40 40 40 40 40 40 40 40 20 19 19 19 19 19 19 19 19 19 19 19
77
78
79 ------
80
81 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
82
83 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
84
85 </help>
86 </tool>
87 <!-- FASTQ-Masker part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->