<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>zcat -f '$input' | fastx_collapser -v -o '$output' 
#if $input.ext == "fastqsanger":
-Q 33
#end if
	</command>

	<inputs>
		<param format="fasta,fastqsanger,fastqsolexa" version="1.0.0" name="input" type="data" label="Library to collapse" />
	</inputs>

    <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines. 
	<tests>
		<test>
			<param version="1.0.0" name="input" value="fasta_collapser1.fasta" />
			<output version="1.0.0" name="output" file="fasta_collapser1.out" />
		</test>
	</tests>
    -->
	<outputs>
		<data format="fasta" version="1.0.0" name="output" metadata_source="input" />
	</outputs>
  <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>