| Next changeset 1:57adb07cccfc (2013-12-03) |
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Commit message:
Uploaded tool tarball. |
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added:
fastq_quality_filter.xml test-data/fastq_qual_filter1.fastq test-data/fastq_qual_filter1a.out test-data/fastq_qual_filter1b.out tool_dependencies.xml |
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| diff -r 000000000000 -r b145b9b26648 fastq_quality_filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_quality_filter.xml Wed Sep 25 11:02:21 2013 -0400 |
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| @@ -0,0 +1,83 @@ +<tool id="cshl_fastq_quality_filter" version="1.0.0" name="Filter by quality"> + <description></description> + <requirements> + <requirement type="package" version="0.0.13">fastx_toolkit</requirement> + </requirements> + <command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output +#if $input.ext == "fastqsanger": +-Q 33 +#end if + </command> + + <inputs> + <param format="fastqsolexa,fastqsanger" version="1.0.0" name="input" type="data" label="Library to filter" /> + + <param version="1.0.0" name="quality" size="4" type="integer" value="20"> + <label>Quality cut-off value</label> + </param> + + <param version="1.0.0" name="percent" size="4" type="integer" value="90"> + <label>Percent of bases in sequence that must have quality equal to / higher than cut-off value</label> + </param> + </inputs> + + <tests> + <test> + <!-- Test1: 100% of bases with quality 33 or higher (pretty steep requirement...) --> + <param version="1.0.0" name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa" /> + <param version="1.0.0" name="quality" value="33"/> + <param version="1.0.0" name="percent" value="100"/> + <output version="1.0.0" name="output" file="fastq_qual_filter1a.out" /> + </test> + <test> + <!-- Test2: 80% of bases with quality 20 or higher --> + <param version="1.0.0" name="input" value="fastq_qual_filter1.fastq" ftype="fastqsolexa"/> + <param version="1.0.0" name="quality" value="20"/> + <param version="1.0.0" name="percent" value="80"/> + <output version="1.0.0" name="output" file="fastq_qual_filter1b.out" /> + </test> + </tests> + + <outputs> + <data format="input" version="1.0.0" name="output" metadata_source="input" /> + </outputs> + + <help> +**What it does** + +This tool filters reads based on quality scores. + +.. class:: infomark + +Using **percent = 100** requires all cycles of all reads to be at least the quality cut-off value. + +.. class:: infomark + +Using **percent = 50** requires the median quality of the cycles (in each read) to be at least the quality cut-off value. + +-------- + +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. + + +**Example**:: + + @CSHL_4_FC042AGOOII:1:2:214:584 + GACAATAAAC + +CSHL_4_FC042AGOOII:1:2:214:584 + 30 30 30 30 30 30 30 30 20 10 + +Using **percent = 50** and **cut-off = 30** - This read will not be discarded (the median quality is higher than 30). + +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). + +Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + </help> +<!-- FASTQ-Quality-Filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> +</tool> |
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| diff -r 000000000000 -r b145b9b26648 test-data/fastq_qual_filter1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_qual_filter1.fastq Wed Sep 25 11:02:21 2013 -0400 |
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| @@ -0,0 +1,36 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:33 +CAATGCCTCCAATTGGTTAATCCCCCTATATATACT ++CSHL_3_FC042AGLLWW:1:2:7:33 +aaaaaaaaaW^U_XaWaa\WMEP^KEZXRPEEEGaa +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1819 +AATTCAAACCACCCCAACCCACACACAGAGATACAA ++CSHL_3_FC042AGLLWW:1:2:7:1819 +a\\QVVVLaaLOEXUWUUEKUULEMUEUUKULIQMU +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa +@CSHL_3_FC042AGLLWW:1:2:8:250 +TGCCGCGCACACTGATGCAATTGGTTAATCCCCCTA ++CSHL_3_FC042AGLLWW:1:2:8:250 +aaaaaaaa^aaaaaabbb[KXPEU[RXZ^JUKRKXE |
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| diff -r 000000000000 -r b145b9b26648 test-data/fastq_qual_filter1a.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_qual_filter1a.out Wed Sep 25 11:02:21 2013 -0400 |
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| @@ -0,0 +1,4 @@ +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa |
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| diff -r 000000000000 -r b145b9b26648 test-data/fastq_qual_filter1b.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_qual_filter1b.out Wed Sep 25 11:02:21 2013 -0400 |
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| @@ -0,0 +1,24 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GTACGCATGACCGAACCCCCCNCCCCCCAATTGGTT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaaaaaaaaabaaaaaaaa]]` +@CSHL_3_FC042AGLLWW:1:2:7:169 +GCAGCAGGCGCGTCAGAGAGCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:169 +a_M^a\Uaaa_M_aaaZZZZZZUZUZaaV\ZUGUUR +@CSHL_3_FC042AGLLWW:1:2:7:1436 +AATTATTTATTAAATTTTAATAATATGGGAGACACT ++CSHL_3_FC042AGLLWW:1:2:7:1436 +a^aaaaaaaaaaaaaaa_U`aaaaa_S_aaaaaVV[ +@CSHL_3_FC042AGLLWW:1:2:7:292 +GGAGAAATACACACAATTGGTTAATCCCCCTATATA ++CSHL_3_FC042AGLLWW:1:2:7:292 +babaaaaaaaUMaaaaaaaaaaa\XEUUEP_]UERE +@CSHL_3_FC042AGLLWW:1:2:7:1875 +GCAAAAGAGTAGTGTACCCCCCCCCCCCCCCCCCCC ++CSHL_3_FC042AGLLWW:1:2:7:1875 +aaaaaaaaaXUXXEXaaaaa`_ZaaaaaaaaaXEXU +@CSHL_3_FC042AGLLWW:1:2:8:624 +ACTGCAATTGGTTAATCCCCCTATATAGCGCTGTGG ++CSHL_3_FC042AGLLWW:1:2:8:624 +aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa |
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| diff -r 000000000000 -r b145b9b26648 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 25 11:02:21 2013 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="fastx_toolkit" version="0.0.13"> + <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |