<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.0">
    <description>(ASCII-Numeric)</description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
    <command>
<![CDATA[
zcat -f < '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset
]]>
    </command>
    <inputs>
        <param format="fastq" 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>

        <param name="offset" type="select" label="FASTQ ASCII offset">
            <option value="33">33</option>
            <option selected="true" value="64">64</option>
        </param>
    </inputs>
    <outputs>
        <data format="fastq" name="output" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <!-- ASCII to NUMERIC -->
            <param name="input" value="fastq_qual_conv1.fastq" />
            <param name="QUAL_FORMAT" value="Numeric quality scores" />
            <param name="offset" value="64" />
            <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" />
            <param name="offset" value="64" />
            <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" />
            <param name="offset" value="64" />
            <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" />
            <param name="offset" value="64" />
            <output name="output" file="fastq_qual_conv2n.out" />
        </test>
    </tests>
    <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

------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    </help>
<!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
</tool>