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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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<tool id="cshl_fastq_quality_converter" name="Quality format converter"> <description>(ASCII-Numeric)</description> <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output</command> <inputs> <param format="fastqsolexa" name="input" type="data" label="Library to convert" /> <param name="QUAL_FORMAT" type="select" label="Desired output format"> <option value="-a">ASCII (letters) quality scores</option> <option value="-n">Numeric quality scores</option> </param> </inputs> <tests> <test> <!-- ASCII to NUMERIC --> <param name="input" value="fastq_qual_conv1.fastq" /> <param name="QUAL_FORMAT" value="Numeric quality scores" /> <output name="output" file="fastq_qual_conv1.out" /> </test> <test> <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output --> <param name="input" value="fastq_qual_conv1.fastq" /> <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> <output name="output" file="fastq_qual_conv1a.out" /> </test> <test> <!-- NUMERIC to ASCII --> <param name="input" value="fastq_qual_conv2.fastq" /> <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> <output name="output" file="fastq_qual_conv2.out" /> </test> <test> <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output --> <param name="input" value="fastq_qual_conv2.fastq" /> <param name="QUAL_FORMAT" value="Numeric quality scores" /> <output name="output" file="fastq_qual_conv2n.out" /> </test> </tests> <outputs> <data format="fastqsolexa" name="output" metadata_source="input" /> </outputs> <help> **What it does** Converts a solexa FASTQ file to/from numeric or ASCII quality format. .. class:: warningmark Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). ----- FASTQ with Numeric quality scores:: @CSHL__2_FC042AGWWWXX:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +CSHL__2_FC042AGWWWXX:8:1:120:202 40 40 40 40 20 40 40 40 40 6 40 40 28 40 40 25 40 20 40 -1 30 40 14 27 40 8 1 3 7 -1 11 10 -1 21 10 8 @CSHL__2_FC042AGWWWXX:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC +CSHL__2_FC042AGWWWXX:8:1:103:1185 40 40 40 40 40 35 33 31 40 40 40 32 30 22 40 -0 9 22 17 14 8 36 15 34 22 12 23 3 10 -0 8 2 4 25 30 2 FASTQ with ASCII quality scores:: @CSHL__2_FC042AGWWWXX:8:1:120:202 ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC +CSHL__2_FC042AGWWWXX:8:1:120:202 hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH @CSHL__2_FC042AGWWWXX:8:1:103:1185 ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC +CSHL__2_FC042AGWWWXX:8:1:103:1185 hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B </help> </tool> <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->