<tool id="cshl_fastx_collapser" name="Collapse">
	<description>sequences</description>
	<command>
cat '$input' |
fastx_collapser
#if $input.ext == "fastqsanger":
 -Q 33
#elif $input.ext == "fastq":
 -Q 64
#end if
 -v -o '$output'
</command>

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

	<tests>
		<test>
			<param name="input" value="fasta_collapser1.fasta" />
			<output name="output" file="fasta_collapser1.out" />
		</test>
	</tests>

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

**What it does**

This tool collapses identical sequences in a FASTQ or 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>
<!-- FASTX-Collapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->