view qiime2-2020.8/qiime_vsearch_dereplicate-sequences.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_vsearch_dereplicate-sequences" name="qiime vsearch dereplicate-sequences"
      version="2020.8">
  <description>Dereplicate sequences.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime vsearch dereplicate-sequences

--i-sequences=$isequences

#if $pderepprefix:
 --p-derep-prefix
#end if

--o-dereplicated-table=odereplicatedtable

--o-dereplicated-sequences=odereplicatedsequences

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp odereplicatedsequences.qza $odereplicatedsequences

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality] The sequences to be dereplicated.         [required]" name="isequences" optional="False" type="data" />
    <param label="--p-derep-prefix: --p-derep-prefix: / --p-no-derep-prefix Merge sequences with identical prefixes. If a sequence is identical to the prefix of two or more longer sequences, it is clustered with the shortest of them. If they are equally long, it is clustered with the most abundant.             [default: False]" name="pderepprefix" selected="False" type="boolean" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: dereplicatedtable.qza" name="odereplicatedtable" />
    <data format="qza" label="${tool.name} on ${on_string}: dereplicatedsequences.qza" name="odereplicatedsequences" />
    
  </outputs>

  <help><![CDATA[
Dereplicate sequences.
###############################################################

Dereplicate sequence data and create a feature table and feature
representative sequences. Feature identifiers in the resulting artifacts
will be the sha1 hash of the sequence defining each feature. If clustering
of features into OTUs is desired, the resulting artifacts can be passed to
the cluster_features_* methods in this plugin.

Parameters
----------
sequences : SampleData[Sequences] | SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]
    The sequences to be dereplicated.
derep_prefix : Bool, optional
    Merge sequences with identical prefixes. If a sequence is identical to
    the prefix of two or more longer sequences, it is clustered with the
    shortest of them. If they are equally long, it is clustered with the
    most abundant.

Returns
-------
dereplicated_table : FeatureTable[Frequency]
    The table of dereplicated sequences.
dereplicated_sequences : FeatureData[Sequence]
    The dereplicated sequences.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>