<tool id="fastaptamer_enrich_1_0_2" name="FASTAptamer-Enrich" version="1.0.2">

	<description>Calculate fold-enrichment of each sequence across populations</description>
	
	<version_command>fastaptamer_enrich -v</version_command>
	
	<command interpreter="perl">fastaptamer_enrich -x $input_x -y $input_y -o $output -f $filter
		# if str(input_z) != ''
			-z "${input_z}"
		# end if
	</command>
	
	<inputs>
		<param name="input_x" type="data" format="fasta" label="Input file X"  help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
		<param name="input_y" type="data" format="fasta" label="Input file Y"  help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
		<param name="input_z" type="data" format="fasta" optional="true"  label="Input file Z"  help="Must use FASTA output from FASTAptamer-Count or FASTAptamer-Cluster"></param>
		<param name="filter" type="float" optional="true" value="0"  label="RPM Threshold Filter" help="Sequences with an aggregate RPM (across all populations) less than supplied value will be excluded from analysis"></param>
 	</inputs>
 	
    <outputs>
    	<data name="output" format="tabular" label="FASTAptamer-Enrich output file"></data>
 	</outputs>

    <help>

.. class:: warningmark

FASTAptamer-Enrich requires FASTA formatted input files generated by FASTAptamer-Count or FASTAptamer-Cluster.

------

**FASTAptamer-Enrich** rapidly calculates "fold-enrichment" values for each sequence across two or three input files.  Output is provided as a tab-delimited file and is formatted to include sequence composition, length, rank, reads, reads per million (RPM), cluster information (if available) and enrichment values for each sequence. 

An optional threshold filter can be applied to exclude sequences with total reads per million (across all input populations) less than the number supplied.

Enrichment is calculated by dividing reads per million of y/x (and z/y and z/x, if a third input file is specified).

------

.. 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>