[2] | 1 | <tool id="cshl_fastq_quality_converter" name="Quality format converter"> |
---|
| 2 | <description>(ASCII-Numeric)</description> |
---|
| 3 | <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
|
---|
| 4 | <command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command> |
---|
| 5 | <inputs> |
---|
| 6 | <param format="fastq" name="input" type="data" label="Library to convert" /> |
---|
| 7 | |
---|
| 8 | <param name="QUAL_FORMAT" type="select" label="Desired output format"> |
---|
| 9 | <option value="-a">ASCII (letters) quality scores</option> |
---|
| 10 | <option value="-n">Numeric quality scores</option> |
---|
| 11 | </param> |
---|
| 12 | |
---|
| 13 | <param name="offset" type="select" label="FASTQ ASCII offset"> |
---|
| 14 | <option value="33">33</option> |
---|
| 15 | <option selected="true" value="64">64</option> |
---|
| 16 | </param> |
---|
| 17 | </inputs> |
---|
| 18 | |
---|
| 19 | <tests> |
---|
| 20 | <test> |
---|
| 21 | <!-- ASCII to NUMERIC --> |
---|
| 22 | <param name="input" value="fastq_qual_conv1.fastq" /> |
---|
| 23 | <param name="QUAL_FORMAT" value="Numeric quality scores" /> |
---|
| 24 | <param name="offset" value="64" /> |
---|
| 25 | <output name="output" file="fastq_qual_conv1.out" /> |
---|
| 26 | </test> |
---|
| 27 | <test> |
---|
| 28 | <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output --> |
---|
| 29 | <param name="input" value="fastq_qual_conv1.fastq" /> |
---|
| 30 | <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> |
---|
| 31 | <param name="offset" value="64" /> |
---|
| 32 | <output name="output" file="fastq_qual_conv1a.out" /> |
---|
| 33 | </test> |
---|
| 34 | <test> |
---|
| 35 | <!-- NUMERIC to ASCII --> |
---|
| 36 | <param name="input" value="fastq_qual_conv2.fastq" /> |
---|
| 37 | <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" /> |
---|
| 38 | <param name="offset" value="64" /> |
---|
| 39 | <output name="output" file="fastq_qual_conv2.out" /> |
---|
| 40 | </test> |
---|
| 41 | <test> |
---|
| 42 | <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output --> |
---|
| 43 | <param name="input" value="fastq_qual_conv2.fastq" /> |
---|
| 44 | <param name="QUAL_FORMAT" value="Numeric quality scores" /> |
---|
| 45 | <param name="offset" value="64" /> |
---|
| 46 | <output name="output" file="fastq_qual_conv2n.out" /> |
---|
| 47 | </test> |
---|
| 48 | </tests> |
---|
| 49 | |
---|
| 50 | <outputs> |
---|
| 51 | <data format="fastq" name="output" metadata_source="input" /> |
---|
| 52 | </outputs> |
---|
| 53 | <help> |
---|
| 54 | |
---|
| 55 | **What it does** |
---|
| 56 | |
---|
| 57 | Converts a Solexa FASTQ file to/from numeric or ASCII quality format. |
---|
| 58 | |
---|
| 59 | .. class:: warningmark |
---|
| 60 | |
---|
| 61 | Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale). |
---|
| 62 | |
---|
| 63 | |
---|
| 64 | ----- |
---|
| 65 | |
---|
| 66 | FASTQ with Numeric quality scores:: |
---|
| 67 | |
---|
| 68 | @CSHL__2_FC042AGWWWXX:8:1:120:202 |
---|
| 69 | ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC |
---|
| 70 | +CSHL__2_FC042AGWWWXX:8:1:120:202 |
---|
| 71 | 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 |
---|
| 72 | @CSHL__2_FC042AGWWWXX:8:1:103:1185 |
---|
| 73 | ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC |
---|
| 74 | +CSHL__2_FC042AGWWWXX:8:1:103:1185 |
---|
| 75 | 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 |
---|
| 76 | |
---|
| 77 | |
---|
| 78 | FASTQ with ASCII quality scores:: |
---|
| 79 | |
---|
| 80 | @CSHL__2_FC042AGWWWXX:8:1:120:202 |
---|
| 81 | ACGATAGATCGGAAGAGCTAGTATGCCGTTTTCTGC |
---|
| 82 | +CSHL__2_FC042AGWWWXX:8:1:120:202 |
---|
| 83 | hhhhThhhhFhh\hhYhTh?^hN[hHACG?KJ?UJH |
---|
| 84 | @CSHL__2_FC042AGWWWXX:8:1:103:1185 |
---|
| 85 | ATCACGATAGATCGGCAGAGCTCGTTTACCGTCTTC |
---|
| 86 | +CSHL__2_FC042AGWWWXX:8:1:103:1185 |
---|
| 87 | hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B |
---|
| 88 | |
---|
| 89 | ------ |
---|
| 90 | |
---|
| 91 | This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
---|
| 92 | |
---|
| 93 | .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
---|
| 94 | |
---|
| 95 | </help> |
---|
| 96 | </tool> |
---|
| 97 | <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |
---|