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