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

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13:887cd4ad8e16

<?xml version="1.0" ?>
<tool id="qiime_vsearch_cluster-features-open-reference" name="qiime vsearch cluster-features-open-reference" version="2019.7">
	<description> -  Open-reference clustering of features.</description>
	<requirements>
		<requirement type="package" version="2019.7">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime vsearch cluster-features-open-reference

--i-sequences=$isequences
--i-table=$itable
--i-reference-sequences=$ireferencesequences
--p-perc-identity="$ppercidentity"

#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-new-reference-sequences=onewreferencesequences
;
cp oclusteredtable.qza $oclusteredtable;
cp oclusteredsequences.qza $oclusteredsequences;
cp onewreferencesequences.qza $onewreferencesequences
	]]></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" min="0" max="1" exclude_min="True" exclude_max="False" value="" type="float"/>
		<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}: newreferencesequences.qza" name="onewreferencesequences"/>
	</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,

    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.

    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-open-reference" name="qiime vsearch cluster-features-open-reference"
      version="2020.8">
  <description> Open-reference clustering of features.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime vsearch cluster-features-open-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-new-reference-sequences=onewreferencesequences

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

;
cp onewreferencesequences.qza $onewreferencesequences

  ]]></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}: newreferencesequences.qza" name="onewreferencesequences" />
    
  </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,

    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.

    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>