<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.1">
    <description>(ASCII-Numeric)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
@CATS@ fastq_quality_converter
$QUAL_FORMAT
-o '$output'
@FQQUAL@
    ]]></command>
    <inputs>
        <expand macro="fastq_input" />

        <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>
    <outputs>
        <data name="output" format="fastq" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <!-- ASCII to NUMERIC -->
            <param name="input" ftype="fastqillumina" 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 (should basically copy the input to the output unchanged) -->
            <param name="input" ftype="fastqillumina" 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" ftype="fastqillumina" 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 (should basically copy the input to the output unchanged) -->
            <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
            <param name="QUAL_FORMAT" value="Numeric quality scores" />
            <output name="output" file="fastq_qual_conv2n.out" />
        </test>
        <test>
            <!-- ASCII to NUMERIC -->
            <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in5.fastq" />
            <param name="QUAL_FORMAT" value="Numeric quality scores" />
            <output name="output" file="fastq_quality_converter-out5.fastq" />
        </test>
        <test>
            <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
            <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in6.fastq" />
            <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
            <output name="output" file="fastq_quality_converter-out6.fastq" />
        </test>
    </tests>
    <help><![CDATA[
**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>
    <expand macro="citations" />
<!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
</tool>