<?xml version="1.0"?>
<tool id="seqtk_trimfq" name="seqtk_trimfq" version="@TOOL_VERSION@.1">
    <description>trim FASTQ using the Phred algorithm</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
seqtk trimfq
#if $mode.mode_select == "quality":
    -q $mode.q
    -l $mode.l
#else:
    -b $mode.b
    -e $mode.e
#end if
'$in_file'
@CONDITIONAL_GZIP_OUT@
    ]]></command>
    <inputs>
        <expand macro="in_faq"/>
        <conditional name="mode">
            <param name="mode_select" type="select" label="Mode for trimming FASTQ File">
                <option value="quality">Quality</option>
                <option value="position">Length/Position</option>
            </param>
            <when value="quality">
                <param argument="-q" type="float" value="0.05" label="Error rate threshold" />
                <param argument="-l" type="integer" value="30" label="Maximally trim down to INT bp" />
            </when>
            <when value="position">
                <param argument="-b" type="integer" value="0" label="Trim INT bp from left" />
                <param argument="-e" type="integer" value="0" label="Trim INT bp from right" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="default" format_source="in_file" label="$in_file.name trimmed"/>
    </outputs>
    <tests>
        <test>
            <param name="in_file" value="seqtk_trimfq.fq" ftype="fastqsanger"/>
            <param name="mode_select" value="quality"/>
            <param name="q" value="0.05"/>
            <param name="l" value="30"/>
            <output name="default" file="seqtk_trimfq_default.fq" ftype="fastqsanger"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_trimfq.fq" ftype="fastqsanger"/>
            <param name="mode_select" value="position"/>
            <param name="b" value="5"/>
            <param name="e" value="5"/>
            <output name="default" file="seqtk_trimfq_be.fq" ftype="fastqsanger"/>
        </test>
        <test>
            <param name="in_file" value="seqtk_trimfq.fq.gz" ftype="fastqsanger.gz"/>
            <param name="mode_select" value="position"/>
            <param name="b" value="5"/>
            <param name="e" value="5"/>
            <output name="default" file="seqtk_trimfq_be.fq.gz" ftype="fastqsanger.gz"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Trim a fastq file based on Phred scores, or by length

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