<?xml version="1.0"?>
<macros>
    <token name="@CATS@">
        #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
            gunzip -c -f '$input' |
        #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
            bzcat -f '$input' |
        #else:
            cat '$input' |
        #end if
    </token>
    <token name="@FQQUAL@">
        <![CDATA[
            #if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
                -Q 33
            #elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2', 'fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
                -Q 64
            #end if
        ]]>
    </token>
    <token name="@GZIP@">
        <![CDATA[
            #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
                | gzip -c
            #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
                | bzip2 -c
            #end if
        ]]>
    </token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>
            <yield />
        </requirements>
    </xml>
    <token name="@VERSION@">0.0.14</token>
    <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
    <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
    <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>
    <token name="@FASTQS@">@SANGER@,@SOLEXA@,@ILLUMINA@</token>
    <token name="@FASTAS@">fasta,fasta.gz</token>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @UNPUBLISHED{agordon,
                    author = "Assaf Gordon",
                    title = "FASTQ/A short-reads pre-processing tools",
                    year = "2010",
                    note = "http://hannonlab.cshl.edu/fastx_toolkit/",
                    url = "http://hannonlab.cshl.edu/fastx_toolkit/"}
            </citation>
        </citations>
    </xml>
    <xml name="fasta_input">
        <param name="input" type="data" format="@FASTAS@" label="Input FASTA file" />
    </xml>
    <xml name="fastq_input">
        <param name="input" type="data" format="@FASTQS@" label="Input FASTQ file" />
    </xml>
    <xml name="fastx_input">
        <param name="input" type="data" format="@FASTAS@,@FASTQS@" label="Input file in FASTA or FASTQ format" />
    </xml>
</macros>