<?xml version="1.0"?>
<tool id="seqtk_fqchk" name="seqtk_fqchk" version="@TOOL_VERSION@.1">
    <description>fastq QC (base/quality summary)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk fqchk
-q $q
'$in_file' | awk '{if(NR<4){print "#"$0}else{print $0}}'
> '$default'
    ]]></command>
    <inputs>
        <expand macro="in_fq"/>
        <param argument="-q" type="integer" value="20" label="Quality values" help="Use 0 to get the distribution of all quality values"/>
    </inputs>
    <outputs>
        <data name="default" format="tabular" label="Quality information for $in_file.name"/>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_fqchk.fq" ftype="fastq"/>
            <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_fqchk.fq.gz" ftype="fastq.gz"/>
            <output name="default" file="seqtk_fqchk.out" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Returns quality score information base-by-base.

::

    @SEQ_ID1
    GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
    +
    !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

each based is examined individually and information reported:

::

    #min_len: 60; max_len: 60; avg_len: 60.00; 15 distinct quality values
    #POS  #bases  %A     %C    %G     %T     %N   avgQ  errQ  %low   %high
    #ALL  60      31.7   16.7  18.3   33.3   0.0  15.1  8.7   66.7   33.3
    1     1       0.0    0.0   100.0  0.0    0.0  0.0   3.0   100.0  0.0
    2     1       100.0  0.0   0.0    0.0    0.0  6.0   6.0   100.0  0.0
    3     1       0.0    0.0   0.0    100.0  0.0  6.0   6.0   100.0  0.0
    4     1       0.0    0.0   0.0    100.0  0.0  9.0   9.0   100.0  0.0
    5     1       0.0    0.0   0.0    100.0  0.0  7.0   7.0   100.0  0.0
    6     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
    7     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
    8     1       0.0    0.0   100.0  0.0    0.0  7.0   7.0   100.0  0.0
    9     1       0.0    0.0   100.0  0.0    0.0  9.0   9.0   100.0  0.0
    10    1       0.0    0.0   0.0    100.0  0.0  9.0   9.0   100.0  0.0

@ATTRIBUTION@
    ]]></help>
    <expand macro="citation" />
</tool>