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<tool id="fastaptamer_cluster_1_0_2" name="FASTAptamer-Cluster" version="1.0.2">

	<description>Cluster closely-related sequences using Levenshtein edit distance.</description>
	
	<version_command>fastaptamer_cluster -v</version_command>
	
	<command interpreter="perl">fastaptamer_cluster -i $input -o $output -d $distance -f $filter > $report
	</command>

	<inputs>
		<param name="input" type="data" format="fasta" label="Input file"  help="Must use FASTA output from FASTAptamer-Count"></param>
		<param name="distance" type="integer" label="Levenshtein Edit Distance" value="1" help="Minimum number of insertions, deletions, or substitutions required to transfer a sequence into another"></param>
		<param name="filter" type="integer" label="Read Filter" optional="true" value="1" help="Only sequences with total reads greater than the value supplied will be clustered."></param> 
 	</inputs>
 	
    <outputs>
    	<data name="output" format="fasta" label="FASTAptamer-Cluster output file"></data>
	<data name="report" format="txt" label="FASTAptamer-Cluster Report"></data>
 	</outputs>
 	
    <help>

.. class:: warningmark

FASTAptamer-Cluster requires a FASTA formatted input file generated by FASTAptamer-Count.

.. class:: warningmark

FASTAptamer-Cluster uses an exhaustive approach to clustering and can take *several* hours to process. For faster processing utilize the "Read Filter" option to exclude low read sequences.

------

**FASTAptamer-Cluster** uses the Levenshtein algorithm to cluster together closely-related sequences based on a user-defined edit distance (*the minimum number of insertions, deletions, or subsitutions required to transform one string into another*). 

FASTAptamer-Cluster begins with the most abundant sequence in a population, referred to as the "seed sequence," and clusters with it every sequence in the file within an edit distance less than or equal to the specified edit distance (Cluster #1). The next most abundant unclustered sequence then serves as the next seed sequence for assembling the second cluster from the remaining sequences (Cluster #2), followed by the next most abundant unclustered sequence (Cluster #3), and so on. This process is iterated until every sequence is clustered.

Output is FASTA formatted with the following information on the FASTA identifier line:

	>Rank-Reads-RPM-Cluster#-RankWithinCluster-EditDistanceFromSeedSequence

.. class:: infomark

The "Read Filter" excludes from the clustering process sequences with a total number of reads less than or equal to the integer supplied. Because of the computational complexity of clustering large datasets, the default filter setting of 1 is designed to eliminate singleton sequences from clustering.

------

.. 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>