<?xml version="1.0" ?>
<tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs" version="2018.4">
	<description> - Join paired-end reads.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
	<![CDATA[
	qiime vsearch join-pairs --i-demultiplexed-seqs=$idemultiplexedseqs

	#if $pminovlen:
	 --p-minovlen=$pminovlen
	#end if

	#if str($ptruncqual):
	 --p-truncqual="$ptruncqual"
	#end if

	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if

	#if str($pminmergelen):
	 --p-minmergelen="$pminmergelen"
	#end if

	#if $pmaxdiffs:
	 --p-maxdiffs=$pmaxdiffs
	#end if

	#if str($pqminout):
	 --p-qminout="$pqminout"
	#end if

	#if str($pmaxmergelen):
	 --p-maxmergelen="$pmaxmergelen"
	#end if

	#if str($pmaxns):
	 --p-maxns="$pmaxns"
	#end if

	#if $pallowmergestagger:
  	 --p-allowmergestagger
  #else
  	--p-no-allowmergestagger
	#end if

	#if $pminlen:
	 --p-minlen=$pminlen
	#end if

	#if $pqmax:
	 --p-qmax=$pqmax
	#end if

	#if str($pmaxee):
	 --p-maxee="$pmaxee"
	#end if

	#if str($pqmin):
	 --p-qmin="$pqmin"
	#end if

	#if $pqmaxout:
	 --p-qmaxout=$pqmaxout
	#end if
	 --o-joined-sequences=ojoinedsequences;

	cp ojoinedsequences.qza $ojoinedsequences;
	]]>
	</command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined.  [required]" name="idemultiplexedseqs" optional="False" type="data"/>

		<param label="--p-truncqual: Truncate sequences at the first base with the specified quality score value or lower. [optional]" name="ptruncqual" optional="True" type="text"/>

		<param label="--p-minlen: Sequences shorter than minlen after truncation are discarded.  [default: 1]" name="pminlen" optional="True" type="integer" value="1"/>
		<param label="--p-maxns: Sequences with more than maxns N characters are discarded.  [optional]" name="pmaxns" optional="True" type="text"/>

		<param label="--p-allowmergestagger: --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" checked="False" type="boolean"/>

		<param label="--p-minovlen: Minimum overlap length of forward and reverse reads for joining.  [default: 10]" name="pminovlen" optional="True" type="integer" value="10"/>
		<param label="--p-maxdiffs: Maximum number of mismatches in the forward/reverse read overlap for joining. [default: 10]" name="pmaxdiffs" optional="True" type="integer" value="10"/>

		<param label="--p-minmergelen: Minimum length of the joined read to be retained.  [optional]" name="pminmergelen" optional="True" type="text"/>
		<param label="--p-maxmergelen: Maximum length of the joined read to be retained.  [optional]" name="pmaxmergelen" optional="True" type="text"/>

		<param label="--p-maxee: Maximum number of expected errors in the joined read to be retained.  [optional]" name="pmaxee" optional="True" type="text"/>

		<param label="--p-qmin: The minimum allowed quality score in the input.  [default: 0]" name="pqmin" optional="True" type="text" value="0"/>
		<param label="--p-qminout: The minimum allowed quality score to use in output.  [default: 0]" name="pqminout" optional="True" type="text" value="0"/>

		<param label="--p-qmax: The maximum allowed quality score in the input.  [default: 41]" name="pqmax" optional="True" type="integer" value="41"/>
		<param label="--p-qmaxout: The maximum allowed quality score to use in output.  [default: 41]" name="pqmaxout" optional="True" type="integer" value="41"/>

		<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}: joined-sequences.qza" name="ojoinedsequences"/>
	</outputs>
	<help>
		<![CDATA[
Join paired-end reads.
-----------------------

Join paired-end sequence reads using vsearch's merge_pairs function. The
qmin, qminout, qmax, and qmaxout parameters should only need to be modified
when working with older fastq sequence data. See the vsearch documentation
for details on how paired-end joining is performed, and for more
information on the parameters to this method.

Parameters
----------
demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
    The demultiplexed paired-end sequences to be joined.
truncqual : Int % Range(0, None), optional
    Truncate sequences at the first base with the specified quality score
    value or lower.
minlen : Int % Range(0, None), optional
    Sequences shorter than minlen after truncation are discarded.
maxns : Int % Range(0, None), optional
    Sequences with more than maxns N characters are discarded.
allowmergestagger : Bool, optional
    Allow joining of staggered read pairs.
minovlen : Int % Range(0, None), optional
    Minimum overlap length of forward and reverse reads for joining.
maxdiffs : Int % Range(0, None), optional
    Maximum number of mismatches in the forward/reverse read overlap for
    joining.
minmergelen : Int % Range(0, None), optional
    Minimum length of the joined read to be retained.
maxmergelen : Int % Range(0, None), optional
    Maximum length of the joined read to be retained.
maxee : Float % Range(0.0, None), optional
    Maximum number of expected errors in the joined read to be retained.
qmin : Int % Range(-5, 2, inclusive_end=True), optional
    The minimum allowed quality score in the input.
qminout : Int % Range(-5, 2, inclusive_end=True), optional
    The minimum allowed quality score to use in output.
qmax : Int % Range(40, 41, inclusive_end=True), optional
    The maximum allowed quality score in the input.
qmaxout : Int % Range(40, 41, inclusive_end=True), optional
    The maximum allowed quality score to use in output.

Returns
-------
joined_sequences : SampleData[JoinedSequencesWithQuality]
    The joined sequences.
    ]]>
	</help>
</tool>