<tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse">
    <description>sequences</description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
    <command>
<![CDATA[
zcat -f < '$input' | fastx_collapser -v -o '$output'
#if $input.ext == "fastqsanger":
    -Q 33
#end if
]]>
    </command>

    <inputs>
        <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" />
    </inputs>
    <outputs>
        <data format="fasta" name="output" metadata_source="input" />
    </outputs>
    <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
    <tests>
        <test>
            <param name="input" value="fasta_collapser1.fasta" />
            <param name="output" file="fasta_collapser1.out" />
        </test>
    </tests>
    -->
    <help>
**What it does**

This tool collapses identical sequences in a FASTA file into a single sequence.

--------

**Example**

Example Input File (Sequence "ATAT" appears multiple times)::

    >CSHL_2_FC0042AGLLOO_1_1_605_414
    TGCG
    >CSHL_2_FC0042AGLLOO_1_1_537_759
    ATAT
    >CSHL_2_FC0042AGLLOO_1_1_774_520
    TGGC
    >CSHL_2_FC0042AGLLOO_1_1_742_502
    ATAT
    >CSHL_2_FC0042AGLLOO_1_1_781_514
    TGAG
    >CSHL_2_FC0042AGLLOO_1_1_757_487
    TTCA
    >CSHL_2_FC0042AGLLOO_1_1_903_769
    ATAT
    >CSHL_2_FC0042AGLLOO_1_1_724_499
    ATAT

Example Output file::

    >1-1
    TGCG
    >2-4
    ATAT
    >3-1
    TGGC
    >4-1
    TGAG
    >5-1
    TTCA

.. class:: infomark

Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded.

The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.

The following output::

    >2-4
    ATAT

means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.


------

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

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