comparison fastaptamer_compare_1.xml @ 1:4795b8673e75 draft default tip

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<tool id="fastaptamer_compare_1_0_2" name="FASTAptamer-Compare" version="1.0.2">

	<description>Compare sequence distribution between two populations.</description>
	
	<version_command>fastaptamer_compare -v</version_command>
	
	<command interpreter="perl">fastaptamer_compare -x $input_x -y $input_y -o $output</command>

	<inputs>
		<param name="input_x" type="data" format="fasta" label="Input file X"  help="Must use FASTA output from FASTAptamer-Count"></param>
		<param name="input_y" type="data" format="fasta" label="Input file Y"  help="Must use FASTA output from FASTAptamer-Count"></param>
 	</inputs>
 	
    <outputs>
    	<data name="output" format="tabular" label="FASTAptamer-Compare output file"></data>
 	</outputs>

    <help>

.. class:: warningmark

FASTAptamer-Compare requires FASTA formatted input files generated by FASTAptamer-Count.


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**FASTAptamer-Compare** facilitates statistical analysis of two populations by rapidly generating a tab-delimited output file that lists each unique sequence along with RPM (reads per million) in each population file (if available) and log(2) of the ratio of their RPM values in each population.  RPM data for both populations can be utilized to generate an XY-scatter plot of sequence distribution across two populations.  FASTAptamer-Compare also facilitates the generation of a histogram of the sequence distribution by creating 102 bins for the log(2) values.  This histogram can provide a quick visual comparison of the two populations: distributions centered around 0 indicate similar populations, while distributions shifted to the left or right indicate overall enrichment or depletion.

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.. 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>