Mercurial > repos > devteam > fastq_quality_filter
annotate fastq_quality_filter.xml @ 1:57adb07cccfc
Removed excess version attributes.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 03 Dec 2013 12:36:13 -0500 |
| parents | b145b9b26648 |
| children | e41385662e5e |
| rev | line source |
|---|---|
| 0 | 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> | |
|
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57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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13 <param format="fastqsolexa,fastqsanger" name="input" type="data" label="Library to filter" /> |
| 0 | 14 |
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57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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15 <param name="quality" size="4" type="integer" value="20"> |
| 0 | 16 <label>Quality cut-off value</label> |
| 17 </param> | |
| 18 | |
|
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57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
19 <param name="percent" size="4" type="integer" value="90"> |
| 0 | 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...) --> | |
|
1
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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27 <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" /> |
|
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
28 <param name="quality" value="33"/> |
|
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
29 <param name="percent" value="100"/> |
|
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
30 <param name="output" file="fastq_qual_filter1a.out" /> |
| 0 | 31 </test> |
| 32 <test> | |
| 33 <!-- Test2: 80% of bases with quality 20 or higher --> | |
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1
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
34 <param name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/> |
|
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
35 <param name="quality" value="20"/> |
|
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
36 <param name="percent" value="80"/> |
|
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
37 <param name="output" file="fastq_qual_filter1b.out" /> |
| 0 | 38 </test> |
| 39 </tests> | |
| 40 | |
| 41 <outputs> | |
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1
57adb07cccfc
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
42 <data format="input" name="output" metadata_source="input" /> |
| 0 | 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> |