<tool id="fastaptamer_count_1_0_2" name="FASTAptamer-Count" version="1.0.2">

	<description>Count, rank, sort and normalize sequence reads in a selection population.</description>
	
	<version_command>fastaptamer_count -v</version_command>
	
	<command interpreter="perl">fastaptamer_count -i $input -o $output</command>

	<inputs>
		<param name="input" type="data" format="fastq" label="Input file"  help="Must be FASTQ and should be pre-processed (filtered for quality and trimmed of constant regions)."></param>
 	</inputs>
 	
    <outputs>
    	<data name="output" format="fasta" label="FASTAptamer-Count output file"></data>
 	</outputs>
    
    <help>

.. class:: warningmark

FASTAptamer-Count requires FASTQ formatted input files.

.. class:: infomark

Input files should be trimmed of constant regions and filtered for only high-quality reads.

------

**FASTAptamer-Count** serves as the gateway to the FASTAptamer suite of bioinformatics tools for combinatorial selections.  

For a given FASTQ input file, FASTAptamer-Count will determine the number of times each sequence was read, normalize sequence frequency to reads per million, and rank and sort sequences by decreasing total reads.

Output is generated as a sorted and non-redundant FASTA formatted file in which each unique sequence generates a FASTA entry with the following information in the description line:

	>RANK-READS-RPM

RANK is the relative abundance of the sequence within the population. In cases where two or more sequences are sampled with equal abundance, FASTAptamer-Count follows standard competition ranking (e.g., “1-2-2-4” where two sequences are tied for second).  READS is the raw number of times a sequence was counted. RPM is “Reads per million,” which is a normalized value that allows for comparison across populations of varying read depth. RPM is calculated as: RPM = (READS/(population size)) x 10^6.

------

.. image:: 
	http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png
	:height: 98
	:width: 300

For more information on FASTAptamer, visit our website_.

FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_.

.. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt
.. _website: http://burkelab.missouri.edu/fastaptamer.html

    </help>

    <citations>
    	<citation type="doi">doi:10.1038/mtna.2015.4</citation>
    </citations>
    
</tool>