Mercurial > repos > fastaptamer > fastaptamer_cluster
changeset 0:307254415eb1 draft
Uploaded
author | fastaptamer |
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date | Tue, 10 Feb 2015 14:30:29 -0500 |
parents | |
children | 8a3bb4734410 |
files | fastaptamer_cluster_1.xml |
diffstat | 1 files changed, 65 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastaptamer_cluster_1.xml Tue Feb 10 14:30:29 2015 -0500 @@ -0,0 +1,65 @@ +<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>