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1 <?xml version="1.0" ?>
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2 <tool id="qiime_vsearch_cluster-features-de-novo" name="qiime vsearch cluster-features-de-novo" version="2018.4">
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3 <description> - De novo clustering of features.</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime vsearch cluster-features-de-novo --p-perc-identity="$ppercidentity" --i-table=$itable --i-sequences=$isequences
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10
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11 #if str($cmdconfig) != 'None':
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12 --cmd-config=$cmdconfig
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13 #end if
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14 --o-clustered-table=oclusteredtable --o-clustered-sequences=oclusteredsequences
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15 #set $pthreads = '${GALAXY_SLOTS:-4}'
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16
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17 #if str($pthreads):
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18 --p-threads="$pthreads"
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19 #end if
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20
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21 ;
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22 cp oclusteredtable.qza $oclusteredtable;
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23 cp oclusteredsequences.qza $oclusteredsequences
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24 ]]>
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25 </command>
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26 <inputs>
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27 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] The sequences corresponding to the features in table. [required]" name="isequences" optional="False" type="data"/>
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28 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to be clustered. [required]" name="itable" optional="False" type="data"/>
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29
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30 <param label="--p-perc-identity: The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter. [required]" name="ppercidentity" optional="False" type="text"/>
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31
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32 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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33 </inputs>
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34 <outputs>
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35 <data format="qza" label="${tool.name} on ${on_string}: clustered-table.qza" name="oclusteredtable"/>
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36 <data format="qza" label="${tool.name} on ${on_string}: clustered-sequences.qza" name="oclusteredsequences"/>
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37 </outputs>
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38 <help>
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39 <![CDATA[
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40 De novo clustering of features.
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41 --------------------------------
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42
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43 Given a feature table and the associated feature sequences, cluster the
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44 features based on user-specified percent identity threshold of their
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45 sequences. This is not a general-purpose de novo clustering method, but
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46 rather is intended to be used for clustering the results of quality-
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47 filtering/dereplication methods, such as DADA2, or for re-clustering a
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48 FeatureTable at a lower percent identity than it was originally clustered
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49 at. When a group of features in the input table are clustered into a single
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50 feature, the frequency of that single feature in a given sample is the sum
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51 of the frequencies of the features that were clustered in that sample.
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52 Feature identifiers and sequences will be inherited from the centroid
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53 feature of each cluster. See the vsearch documentation for details on how
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54 sequence clustering is performed.
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55
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56 Parameters
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57 ----------
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58 sequences : FeatureData[Sequence]
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59 The sequences corresponding to the features in table.
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60 table : FeatureTable[Frequency]
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61 The feature table to be clustered.
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62 perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True)
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63 The percent identity at which clustering should be performed. This
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64 parameter maps to vsearch's --id parameter.
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65
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66 Returns
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67 -------
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68 clustered_table : FeatureTable[Frequency]
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69 The table following clustering of features.
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70 clustered_sequences : FeatureData[Sequence]
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71 Sequences representing clustered features.
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72 ]]>
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73 </help>
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74 <macros>
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75 <import>qiime_citation.xml</import>
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76 </macros>
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77 <expand macro="qiime_citation" />
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78 </tool>
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