Mercurial > repos > fastaptamer > fastaptamer_cluster
comparison fastaptamer_cluster_1.xml @ 0:307254415eb1 draft
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| author | fastaptamer |
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| date | Tue, 10 Feb 2015 14:30:29 -0500 |
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| -1:000000000000 | 0:307254415eb1 |
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| 1 <tool id="fastaptamer_cluster_1_0_2" name="FASTAptamer-Cluster" version="1.0.2"> | |
| 2 | |
| 3 <description>Cluster closely-related sequences using Levenshtein edit distance.</description> | |
| 4 | |
| 5 <version_command>fastaptamer_cluster -v</version_command> | |
| 6 | |
| 7 <command interpreter="perl">fastaptamer_cluster -i $input -o $output -d $distance -f $filter > $report | |
| 8 </command> | |
| 9 | |
| 10 <inputs> | |
| 11 <param name="input" type="data" format="fasta" label="Input file" help="Must use FASTA output from FASTAptamer-Count"></param> | |
| 12 <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> | |
| 13 <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> | |
| 14 </inputs> | |
| 15 | |
| 16 <outputs> | |
| 17 <data name="output" format="fasta" label="FASTAptamer-Cluster output file"></data> | |
| 18 <data name="report" format="txt" label="FASTAptamer-Cluster Report"></data> | |
| 19 </outputs> | |
| 20 | |
| 21 <help> | |
| 22 | |
| 23 .. class:: warningmark | |
| 24 | |
| 25 FASTAptamer-Cluster requires a FASTA formatted input file generated by FASTAptamer-Count. | |
| 26 | |
| 27 .. class:: warningmark | |
| 28 | |
| 29 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. | |
| 30 | |
| 31 ------ | |
| 32 | |
| 33 **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*). | |
| 34 | |
| 35 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. | |
| 36 | |
| 37 Output is FASTA formatted with the following information on the FASTA identifier line: | |
| 38 | |
| 39 >Rank-Reads-RPM-Cluster#-RankWithinCluster-EditDistanceFromSeedSequence | |
| 40 | |
| 41 .. class:: infomark | |
| 42 | |
| 43 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. | |
| 44 | |
| 45 ------ | |
| 46 | |
| 47 .. image:: | |
| 48 http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png | |
| 49 :height: 98 | |
| 50 :width: 300 | |
| 51 | |
| 52 For more information on FASTAptamer, visit our website_. | |
| 53 | |
| 54 FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_. | |
| 55 | |
| 56 .. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt | |
| 57 .. _website: http://burkelab.missouri.edu/fastaptamer.html | |
| 58 | |
| 59 </help> | |
| 60 | |
| 61 <citations> | |
| 62 <citation type="doi">doi:10.1038/mtna.2015.4</citation> | |
| 63 </citations> | |
| 64 | |
| 65 </tool> |