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1 <tool id="cluster_otu" name="Cluster OTU" version="1.0.0">
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2 <description>Cluster OTUs</description>
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3 <command>
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4 usearch -cluster_otus $input -otus $output -otuid $radius 2>1
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5 </command>
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6
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7 <inputs>
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8 <param name="input" type="data" format="fasta" label="Input sequence file"
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9 help="Size annotation is required, see description below!"/>
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10 <param name="radius" type='float' value='0.97' label='Minimum cluster radius'
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11 help="default=0.97, corresponds to minimum of 97% sequence identity" />
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12 </inputs>
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13
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14 <outputs>
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15 <data name='output' format="fasta" />
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16 </outputs>
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17
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18 <help>
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19 ===========
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20 Description
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21 ===========
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22
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23 Performs OTU clustering using the USEARCH-Tool-Suite_.
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24
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25 .. _USEARCH-Tool-Suite: http://www.drive5.com/usearch/
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26
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27 -----
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28
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29 -----
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30 Input
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31 -----
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32
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33 FASTA file with size annotation in the input line, e.g. >sequenceXXXX;size=1443;
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34
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35 .. class:: warningmark
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36
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37 Size annotation is required.
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38
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39 ----------
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40 Parameters
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41 ----------
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42
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43 radius
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44 (Usearch v7.0.1002 and earlier) specifies the OTU 'radius' as the minimum identity between an OTU member sequence and the representative sequence as a fractional identity 0.0 to 1.0. Default is 0.97, which corresponds to a minimum identity of 97%.
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45
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46 ------
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47 Output
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48 ------
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49
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50 FASTA output of the representative sequences.
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51
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52 .. class:: warningmark
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53
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54 If there is a "size=XX" annotation in the identifier line of the output file, please note this is NOT the number of sequences in this cluster. The size annotation is then coming from the input file.
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55
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56 -----
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57
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58 =========
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59 Resources
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60 =========
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61
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62 UPARSE_ (OTU Clustering)
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63
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64 .._UPARSE: http://drive5.com/usearch/manual/cluster_otus.html
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65
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66 **Author**
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67
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68 Robert C. Edgar (bob@drive5.com)
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69
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70 **Wrapper Author**
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71
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72 QFAB Bioinformatics (support@qfab.org)
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73 </help>
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74 <tests>
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75 <test>
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76 <param name="input" value="seqs_derep.fasta" />
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77 <param name="radius" value="0.97" />
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78 <output name="output" file="seqs_otus.fasta" ftype="fasta" lines_diff="10" />
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79 </test>
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80 </tests>
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81 </tool>
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