<?xml version="1.0"?>
<tool id="seqtk_seq" name="seqtk_seq" version="@TOOL_VERSION@.3">
    <description>common transformation of FASTA/Q</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk seq -q $q
-X $X
#if $n:
    -n '$n'
#end if
-l $l
-Q $Q
-s $s
-f $f
#if $M:
    -M '$M'
#end if
-L $L
$c
$r
$A
$C
$N
$x1
$x2
#if $in_file.is_of_type('fastqillumina')
    -V
#end if
'$in_file'
@CONDITIONAL_GZIP_OUT@
    ]]></command>
    <inputs>
        <expand macro="in_faq"/>
        <param argument="-q" type="integer" value="0" label="Mask bases with quality lower than INT" />
        <param argument="-X" type="integer" value="255" label="Mask bases with quality higher than INT" />
        <param argument="-n" type="text" value="0" label="Masked bases converted to CHAR; 0 for lowercase" />
        <param argument="-l" type="integer" value="0" label="Number of residues per line; 0 for 2^32-1" />
        <param argument="-Q" type="integer" value="33" label="Quality shift: ASCII-INT gives base quality" />
        <param argument="-s" type="integer" value="11" label="Random seed" help="Effective with -f" />
        <param argument="-f" type="float" value="1" label="Sample fraction of sequences" />
        <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" />
        <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" />
        <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" />
        <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Reverse complement" />
        <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Force FASTA output (discard quality)" />
        <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" />
        <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
        <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
        <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
    </inputs>
    <outputs>
        <data name="default" format_source="in_file" />
    </outputs>
    <tests>
        <!-- This is a sorry excuse for a test for a tool which does way more
             than it should, but upstream decided to put a TON of functionality
             into a single tool rather than using the single responsibility
             principle. -->
        <test>
            <param name="in_file" value="seqtk_seq.fa"/>
            <param name="r" value="True"/>
            <param name="n" value=""/>
            <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_seq.fa.gz" ftype="fasta.gz"/>
            <param name="r" value="True"/>
            <param name="n" value=""/>
            <output name="default" file="seqtk_seq_revcom.fa.gz" ftype="fasta.gz"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Various utilities for transforming FASTA/Q data

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