root/galaxy-central/tools/fastx_toolkit/fastx_reverse_complement.xml @ 3

<tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
        <description></description>
        <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
        <command>zcat -f '$input' | fastx_reverse_complement -v -o $output</command>
        <inputs>
                <param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" />
        </inputs>

        <tests>
                <test>
                        <!-- Reverse-complement a FASTA file -->
                        <param name="input" value="fastx_rev_comp1.fasta" /> 
                        <output name="output" file="fastx_reverse_complement1.out" />
                </test>
                <test>
                        <!-- Reverse-complement a FASTQ file -->
                        <param name="input" value="fastx_rev_comp2.fastq" />
                        <output name="output" file="fastx_reverse_complement2.out" />
                </test>
        </tests>

  
        <outputs>
                <data format="input" name="output" metadata_source="input" />
        </outputs>

<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>