| Next changeset 1:0d1cf9024f0e (2016-12-26) |
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Commit message:
Uploaded |
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added:
rapidcluster.xml |
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| diff -r 000000000000 -r 12f2dd9ac1fd rapidcluster.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapidcluster.xml Mon Dec 26 11:04:51 2016 -0500 |
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| @@ -0,0 +1,52 @@ +<tool id="rapidcluster_2" name="RapidCluster" version="2"> + + <description>Cluster closely-related sequences using Levenshtein edit distance filtering.</description> + + <version_command>rapidcluster -v</version_command> + + <command interpreter="perl">rapidcluster -i $input -o $output -d $distance -f $filter -c $max_clusters > $report + </command> + + <inputs> + <param name="input" type="data" format="fasta" label="Input file" help="Must use FASTA output from FASTAptamer-Count"></param> + <param name="distance" type="integer" label="Levenshtein Edit Distance" value="1" help="Minimum number of insertions, deletions, or substitutions required to transfer a sequence into another"></param> + <param name="filter" type="integer" label="Read Filter" optional="true" value="1" help="Only sequences with total reads greater than the value supplied will be clustered."></param> + <param name="max_clusters" type="integer" label="Maximum number of clusters to find" optional="true" value="500" help="Script will stop after finding this much clusters"></param> + </inputs> + + <outputs> + <data name="output" format="fasta" label="$input RapidCluster output"></data> + <data name="report" format="txt" label="$input RapidCluster Report"></data> + </outputs> + + <help> + +.. class:: warningmark + +RapidCluster requires a FASTA formatted input file generated by FASTAptamer-Count. + +.. class:: warningmark + +RapidCluster 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 and define a reasonable number of clusters to find. + +------ + +This version does not calculate exact Levenshtein distance for each pair of sequences, instead it simply checks if this distance is lower or greater than user-defined value. This makes script much faster for clustering highly-similar sequences. + +RapidCluster 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. + +------ + + + </help> + + +</tool> |