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