<?xml version="1.0" ?>
<tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref" version="2018.4">
	<description> - Reference-based chimera filtering with vsearch.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
		<![CDATA[
		qiime vsearch uchime-ref --i-table=$itable --i-sequences=$isequences --i-reference-sequences=$ireferencesequences --o-nonchimeras=ononchimeras --o-stats=ostats

#if $pmindiffs:
 --p-mindiffs=$pmindiffs
#end if

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

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


#if $pdn:
 --p-dn=$pdn
#end if
 --o-chimeras=ochimeras
#if str($cmdconfig) != 'None':
 --cmd-config=$cmdconfig
#end if

#if $pminh:
 --p-minh=$pminh
#end if

#if $pmindiv:
 --p-mindiv=$pmindiv
#end if

#if $pxn:
 --p-xn=$pxn
#end if
;
cp ononchimeras.qza $ononchimeras;
cp ostats.qza $ostats;
cp ochimeras.qza $ochimeras
	]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table (used for computing total feature abundances).  [required]" name="itable" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-reference-sequences: FeatureData[Sequence] The non-chimeric reference sequences. [required]" name="ireferencesequences" optional="False" type="data"/>

		<param label="--p-dn: No vote pseudo-count, corresponding to the parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" value="1.4"/>

		<param label="--p-mindiffs: Minimum number of differences per segment. [default: 3]" name="pmindiffs" optional="True" type="integer" value="3"/>
		<param label="--p-mindiv: Minimum divergence from closest parent. [default: 0.8]" name="pmindiv" optional="True" type="float" value="0.8"/>
		<param label="--p-minh: Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" value="0.28"/>

		<param label="--p-xn: No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" value="8.0"/>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: non-chimeras.qza" name="ononchimeras"/>
		<data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
		<data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
	</outputs>
	<help>
		<![CDATA[
Reference-based chimera filtering with vsearch.
------------------------------------------------

Apply the vsearch uchime_ref method to identify chimeric feature sequences.
The results of this method can be used to filter chimeric features from the
corresponding feature table. For additional details, please refer to the
vsearch documentation.

Parameters
----------
sequences : FeatureData[Sequence]
    The feature sequences to be chimera-checked.
table : FeatureTable[Frequency]
    Feature table (used for computing total feature abundances).
reference_sequences : FeatureData[Sequence]
    The non-chimeric reference sequences.
dn : Float % Range(0.0, None), optional
    No vote pseudo-count, corresponding to the parameter n in the chimera
    scoring function.
mindiffs : Int % Range(1, None), optional
    Minimum number of differences per segment.
mindiv : Float % Range(0.0, None), optional
    Minimum divergence from closest parent.
minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Minimum score (h). Increasing this value tends to reduce the number of
    false positives and to decrease sensitivity.
xn : Float % Range(1.0, None, inclusive_start=False), optional
    No vote weight, corresponding to the parameter beta in the scoring
    function.

Returns
-------
chimeras : FeatureData[Sequence]
    The chimeric sequences.
nonchimeras : FeatureData[Sequence]
    The non-chimeric sequences.
stats : UchimeStats
    Summary statistics from chimera checking.
		]]>
	</help>
</tool>