<tool id="cshl_fastx_uncollapser" name="Uncollapse" version="1.0.0">
	<description>sequences</description>
	<command>
cat '$input' | 
fastx_uncollapser -v -o '$output'
</command>
	<inputs>
		<param format="fasta" name="input" type="data" label="Collapsed FASTA file" />
	</inputs>

	<tests>
		<test>
			<param name="input" value="fasta_uncollapser1.fasta" />
			<output name="output" file="fasta_uncollapser1.out" />
		</test>
	</tests>

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

**What it does**

This tool uncollapses a previously-collapsed FASTA file. It reads each collapsed sequence and generates multiple sequences based on the collapsed read count.

--------

**Example**

Example Input - a collapsed FASTA file (Sequence "ATAT" has four collapsed reads)::

    >1-1
    TGCG
    >2-4
    ATAT

Example Output - uncollapsed FASTA file (Sequence "ATAT" now appears as 4 separate sequences):: 

    >1
    TGCG
    >2
    ATAT
    >3
    ATAT
    >4
    ATAT
    >5
    ATAT
    
.. class:: infomark

The original sequence id (with the read counts) are discarded, with the sequence given a numerical name. 

-----

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

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    
</help>
</tool>
<!-- FASTX-Uncollapser is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->