<?xml version="1.0" ?>
<tool id="qiime_quality-control_exclude-seqs" name="qiime quality-control exclude-seqs" version="2018.4">
	<description> - Exclude sequences by alignment</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
    <![CDATA[
    qiime quality-control exclude-seqs --i-reference-sequences=$ireferencesequences --i-query-sequences=$iquerysequences
#if str($pevalue):
 --p-evalue="$pevalue"
#end if

#if $ppercidentity:
 --p-perc-identity=$ppercidentity
#end if

#if $ppercqueryaligned:
 --p-perc-query-aligned=$ppercqueryaligned
#end if

#if str($cmdconfig) != 'None':
 --cmd-config=$cmdconfig
#end if
 --o-sequence-hits=osequencehits --o-sequence-misses=osequencemisses
#if str($pmethod) != 'None':
 --p-method=$pmethod
#end if

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

#if str($pthreads):
 --p-threads="$pthreads"
#end if
;
cp osequencehits.qza $osequencehits;
cp osequencemisses.qza $osequencemisses;
  ]]>
  </command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-query-sequences: FeatureData[Sequence] Sequences to test for exclusion  [required]" name="iquerysequences" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-reference-sequences: FeatureData[Sequence] Reference sequences to align against feature sequences  [required]" name="ireferencesequences" optional="False" type="data"/>

		<param label="--p-method: Alignment method to use for matching feature
                                  sequences against reference sequences
                                  [default: blast]" name="pmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="vsearch">vsearch</option>
			<option value="blast">blast</option>
			<option value="blastn-short">blastn-short</option>
		</param>

		<param label="--p-perc-identity: Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]  [default: 0.97]" name="ppercidentity" optional="True" type="float" value="0.97"/>
		<param label="--p-evalue: BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default.  [optional]" name="pevalue" optional="True" type="text"/>
		<param label="--p-perc-query-aligned: Percent of query sequence that must align to reference in order to be accepted as a hit. [default: 0.97]" name="ppercqueryaligned" optional="True" type="float" value="0.97"/>

		<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 ${on_string}: sequence-hits.qza" name="osequencehits"/>
		<data format="qza" label="${tool.name} on ${on_string}: sequence-misses.qza" name="osequencemisses"/>
	</outputs>
	<help><![CDATA[
Exclude sequences by alignment
-------------------------------

This method aligns feature sequences to a set of reference sequences to
identify sequences that hit/miss the reference within a specified
perc_identity, evalue, and perc_query_aligned. This method could be used to
define a positive filter, e.g., extract only feature sequences that align
to a certain clade of bacteria; or to define a negative filter, e.g.,
identify sequences that align to contaminant or human DNA sequences that
should be excluded from subsequent analyses. Note that filtering is
performed based on the perc_identity, perc_query_aligned, and evalue
thresholds (the latter only if method==BLAST and an evalue is set). Set
perc_identity==0 and/or perc_query_aligned==0 to disable these filtering
thresholds as necessary.

Parameters
----------
query_sequences : FeatureData[Sequence]
    Sequences to test for exclusion
reference_sequences : FeatureData[Sequence]
    Reference sequences to align against feature sequences
method : Str % Choices({'blast', 'blastn-short', 'vsearch'}), optional
    Alignment method to use for matching feature sequences against
    reference sequences
perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Reject match if percent identity to reference is lower. Must be in
    range [0.0, 1.0]
evalue : Float, optional
    BLAST expectation (E) value threshold for saving hits. Reject if E
    value is higher than threshold. This threshold is disabled by default.
perc_query_aligned : Float, optional
    Percent of query sequence that must align to reference in order to be
    accepted as a hit.

Returns
-------
sequence_hits : FeatureData[Sequence]
    Subset of feature sequences that align to reference sequences
sequence_misses : FeatureData[Sequence]
    Subset of feature sequences that do not align to reference sequences
      ]]>
	</help>
<macros>
	<import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation" />
</tool>