<tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement">
    <description></description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
    <command>
<![CDATA[
zcat -f < '$input' | fastx_reverse_complement -v -o '$output'
#if $input.ext == "fastqsanger":
    -Q 33
#end if
]]>
    </command>
    <inputs>
        <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
    </inputs>
    <outputs>
        <data format_source="input" name="output" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <!-- Reverse-complement a FASTA file -->
            <param name="input" value="fastx_rev_comp1.fasta" />
            <output name="output" ftype="fasta" file="fastx_reverse_complement1.out" />
        </test>
        <test>
            <!-- Reverse-complement a FASTQ file -->
            <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
            <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" />
        </test>
    </tests>
    <help>
**What it does**

This tool reverse-complements each sequence in a library.
If the library is a FASTQ, the quality-scores are also reversed.

--------

**Example**

Input FASTQ file::

    @CSHL_1_FC42AGWWWXX:8:1:3:740
    TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
    +CSHL_1_FC42AGWWWXX:8:1:3:740
    33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26


Output FASTQ file::

    @CSHL_1_FC42AGWWWXX:8:1:3:740
    TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
    +CSHL_1_FC42AGWWWXX:8:1:3:740
    26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33

------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    </help>
</tool>