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<tool id="seqtk_seq" name="Convert to FASTA (seqtk)" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.0-r68">seqtk</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        seqtk seq
              $shift_quality
              -q $quality_min
              -X $quality_max
              -a "$input1" > "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" format="fastq" />
        <param name="shift_quality" type="boolean" label="Shift quality"
            truevalue="-V" falsevalue=""
            help="shift quality by '(-Q) - 33' (-V)" />
        <param name="quality_min" type="integer" label="Mask bases with quality lower than"
            value="0" min="0" max="255" help="(-q)" />
        <param name="quality_max" type="integer" label="Mask bases with quality higher than"
            value="255" min="0" max="255" help="(-X)" />
    </inputs>
    <outputs>
        <data name="output1" format="fasta" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="2.fastq"/>
            <output name="output1" file="2.fasta"/>
        </test>
    </tests>
    <help><![CDATA[
        
Usage:   seqtk seq [options] <in.fq>|<in.fa>

Options: -q INT    mask bases with quality lower than INT [0]
         -X INT    mask bases with quality higher than INT [255]
         -n CHAR   masked bases converted to CHAR; 0 for lowercase [0]
         -l INT    number of residues per line; 0 for 2^32-1 [0]
         -Q INT    quality shift: ASCII-INT gives base quality [33]
         -s INT    random seed (effective with -f) [11]
         -f FLOAT  sample FLOAT fraction of sequences [1]
         -M FILE   mask regions in BED or name list FILE [null]
         -L INT    drop sequences with length shorter than INT [0]
         -c        mask complement region (effective with -M)
         -r        reverse complement
         -A        force FASTA output (discard quality)
         -C        drop comments at the header lines
         -N        drop sequences containing ambiguous bases
         -1        output the 2n-1 reads only
         -2        output the 2n reads only
         -V        shift quality by '(-Q) - 33'
         -U        convert all bases to uppercases


    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubseqtk,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {seqtk},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/lh3/seqtk},
}</citation>
    </citations>
</tool>