comparison qiime2/qiime_vsearch_cluster-features-closed-reference.xml @ 14:a0a8d77a991c draft

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13:887cd4ad8e16

<?xml version="1.0" ?>
<tool id="qiime_vsearch_cluster-features-closed-reference" name="qiime vsearch cluster-features-closed-reference" version="2019.7">
	<description> -  Closed-reference clustering of features.</description>
	<requirements>
		<requirement type="package" version="2019.7">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime vsearch cluster-features-closed-reference
--i-sequences=$isequences
--i-table=$itable
--i-reference-sequences=$ireferencesequences

#if str($ppercidentity):
  --p-perc-identity="$ppercidentity"
#end if

#if str($pstrand) != 'None':
 --p-strand=$pstrand
#end if

#set $pthreads = '${GALAXY_SLOTS:-4}'

#if str($pthreads):
 --p-threads="$pthreads"
#end if

--o-clustered-table=oclusteredtable
--o-clustered-sequences=oclusteredsequences
--o-unmatched-sequences=ounmatchedsequences
;
cp oclusteredtable.qza $oclusteredtable;
cp oclusteredsequences.qza $oclusteredsequences;
cp ounmatchedsequences.qza $ounmatchedsequences
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data"/>
		<param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch's --id parameter.                                [required]" name="ppercidentity" optional="False" type="float" value="" min="0" max="1" exclude_max="False" />
		<param label="--p-strand: " name="pstrand" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="plus">plus</option>
			<option value="both">both</option>
		</param>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable"/>
		<data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences"/>
		<data format="qza" label="${tool.name} on ${on_string}: unmatchedsequences.qza" name="ounmatchedsequences"/>
	</outputs>
	<help><![CDATA[
Open-reference clustering of features.
######################################

Given a feature table and the associated feature sequences, cluster the
features against a reference database based on user-specified percent
identity threshold of their sequences. Any sequences that don't match are
then clustered de novo. This is not a general-purpose clustering method,
but rather is intended to be used for clustering the results of quality-
filtering/dereplication methods, such as DADA2, or for re-clustering a
FeatureTable at a lower percent identity than it was originally clustered
at. When a group of features in the input table are clustered into a single
feature, the frequency of that single feature in a given sample is the sum
of the frequencies of the features that were clustered in that sample.
Feature identifiers will be inherited from the centroid feature of each
cluster. For features that match a reference sequence, the centroid feature
is that reference sequence, so its identifier will become the feature
identifier. The clustered_sequences result will contain feature
representative sequences that are derived from the sequences input for all
features in clustered_table. This will always be the most abundant sequence
in the cluster. The new_reference_sequences result will contain the entire
reference database, plus feature representative sequences for any de novo
features. This is intended to be used as a reference database in subsequent
iterations of cluster_features_open_reference, if applicable. See the
vsearch documentation for details on how sequence clustering is performed.

Parameters
----------
sequences : FeatureData[Sequence]
    The sequences corresponding to the features in table.

    The percent identity at which clustering should be performed. This
    parameter maps to vsearch's --id parameter.
strand : Str % Choices('plus', 'both'), optional
    Search plus (i.e., forward) or both (i.e., forward and reverse
    complement) strands.

Returns
-------
clustered_table : FeatureTable[Frequency]
    The table following clustering of features.
clustered_sequences : FeatureData[Sequence]
    Sequences representing clustered features.
new_reference_sequences : FeatureData[Sequence]
    The new reference sequences. This can be used for subsequent runs of
    open-reference clustering for consistent definitions of features across
    open-reference feature tables.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>

14:a0a8d77a991c

<?xml version="1.0" ?>
<tool id="qiime_vsearch_cluster-features-closed-reference" name="qiime vsearch cluster-features-closed-reference"
      version="2020.8">
  <description> Closed-reference clustering of features.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime vsearch cluster-features-closed-reference

--i-sequences=$isequences

--i-table=$itable

--i-reference-sequences=$ireferencesequences

--p-perc-identity=$ppercidentity

#if str($pstrand) != 'None':
--p-strand=$pstrand
#end if

--p-threads=$pthreads

--o-clustered-table=oclusteredtable

--o-clustered-sequences=oclusteredsequences

--o-unmatched-sequences=ounmatchedsequences

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

;
cp ounmatchedsequences.qza $ounmatchedsequences

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences corresponding to the features in table.                                    [required]" name="isequences" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to be clustered.        [required]" name="itable" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The sequences to use as cluster centroids. [required]" name="ireferencesequences" optional="False" type="data" />
    <param label="--p-perc-identity: PROPORTION Range(0, 1, inclusive_start=False, inclusive_end=True)   The percent identity at which clustering should be performed. This parameter maps to vsearch\'s --id parameter.                                [required]" name="ppercidentity" optional="False" type="text" />
    <param label="--p-strand: " name="pstrand" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="plus">plus</option>
      <option value="both">both</option>
    </param>
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: clusteredtable.qza" name="oclusteredtable" />
    <data format="qza" label="${tool.name} on ${on_string}: clusteredsequences.qza" name="oclusteredsequences" />
    <data format="qza" label="${tool.name} on ${on_string}: unmatchedsequences.qza" name="ounmatchedsequences" />
    
  </outputs>

  <help><![CDATA[
 Closed-reference clustering of features.
###############################################################

Given a feature table and the associated feature sequences, cluster the
features against a reference database based on user-specified percent
identity threshold of their sequences. This is not a general-purpose
closed-reference clustering method, but rather is intended to be used for
clustering the results of quality-filtering/dereplication methods, such as
DADA2, or for re-clustering a FeatureTable at a lower percent identity than
it was originally clustered at. When a group of features in the input table
are clustered into a single feature, the frequency of that single feature
in a given sample is the sum of the frequencies of the features that were
clustered in that sample. Feature identifiers will be inherited from the
centroid feature of each cluster. See the vsearch documentation for details
on how sequence clustering is performed.

Parameters
----------
sequences : FeatureData[Sequence]
    The sequences corresponding to the features in table.

    The percent identity at which clustering should be performed. This
    parameter maps to vsearch's --id parameter.
strand : Str % Choices('plus', 'both'), optional
    Search plus (i.e., forward) or both (i.e., forward and reverse
    complement) strands.
threads : Int % Range(0, 256, inclusive_end=True), optional
    The number of threads to use for computation. Passing 0 will launch one
    thread per CPU core.

Returns
-------
clustered_table : FeatureTable[Frequency]
    The table following clustering of features.
clustered_sequences : FeatureData[Sequence]
    The sequences representing clustered features, relabeled by the
    reference IDs.
unmatched_sequences : FeatureData[Sequence]
    The sequences which failed to match any reference sequences. This
    output maps to vsearch's --notmatched parameter.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>