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comparison fastq_quality_filter.xml @ 0:b145b9b26648

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author devteam
date Wed, 25 Sep 2013 11:02:21 -0400
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1 <tool id="cshl_fastq_quality_filter" version="1.0.0" name="Filter by quality">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output
7 #if $input.ext == "fastqsanger":
8 -Q 33
9 #end if
10 </command>
11
12 <inputs>
13 <param format="fastqsolexa,fastqsanger" version="1.0.0" name="input" type="data" label="Library to filter" />
14
15 <param version="1.0.0" name="quality" size="4" type="integer" value="20">
16 <label>Quality cut-off value</label>
17 </param>
18
19 <param version="1.0.0" name="percent" size="4" type="integer" value="90">
20 <label>Percent of bases in sequence that must have quality equal to / higher than cut-off value</label>
21 </param>
22 </inputs>
23
24 <tests>
25 <test>
26 <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) -->
27 <param version="1.0.0" name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" />
28 <param version="1.0.0" name="quality" value="33"/>
29 <param version="1.0.0" name="percent" value="100"/>
30 <output version="1.0.0" name="output" file="fastq_qual_filter1a.out" />
31 </test>
32 <test>
33 <!-- Test2: 80% of bases with quality 20 or higher -->
34 <param version="1.0.0" name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/>
35 <param version="1.0.0" name="quality" value="20"/>
36 <param version="1.0.0" name="percent" value="80"/>
37 <output version="1.0.0" name="output" file="fastq_qual_filter1b.out" />
38 </test>
39 </tests>
40
41 <outputs>
42 <data format="input" version="1.0.0" name="output" metadata_source="input" />
43 </outputs>
44
45 <help>
46 **What it does**
47
48 This tool filters reads based on quality scores.
49
50 .. class:: infomark
51
52 Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value.
53
54 .. class:: infomark
55
56 Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value.
57
58 --------
59
60 Quality score distribution (of all cycles) is calculated for each read. If it is lower than the quality cut-off value - the read is discarded.
61
62
63 **Example**::
64
65 @CSHL_4_FC042AGOOII:1:2:214:584
66 GACAATAAAC
67 +CSHL_4_FC042AGOOII:1:2:214:584
68 30 30 30 30 30 30 30 30 20 10
69
70 Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30).
71
72 Using **percent = 90** and **cut-off = 30** - This read will be discarded (90% of the cycles do no have quality equal to / higher than 30).
73
74 Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20).
75
76 ------
77
78 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
79
80 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
81 </help>
82 <!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
83 </tool>