<?xml version="1.0" ?>
<tool id="qiime_vsearch_join-pairs" name="qiime vsearch join-pairs"
      version="2020.8">
  <description>Join paired-end reads.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime vsearch join-pairs

--i-demultiplexed-seqs=$idemultiplexedseqs

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

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

--p-minovlen=$pminovlen

--p-maxdiffs=$pmaxdiffs

#if str($pminmergelen):
  --p-minmergelen=$pminmergelen
#end if
#if str($pmaxmergelen):
  --p-maxmergelen=$pmaxmergelen
#end if
#if str($pmaxee):
  --p-maxee=$pmaxee
#end if
--p-qmin=$pqmin

--p-qminout=$pqminout

--p-qmax=$pqmax

--p-qmaxout=$pqmaxout

--p-threads=$pthreads

--o-joined-sequences=ojoinedsequences

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

;
cp ojoinedsequences.qza $ojoinedsequences

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The demultiplexed paired-end sequences to be joined. [required]" name="idemultiplexedseqs" optional="False" type="data" />
    <param label="--p-truncqual: INTEGER  Truncate sequences at the first base with the Range(0, None)       specified quality score value or lower.    [optional]" name="ptruncqual" optional="False" type="text" />
    <param label="--p-minlen: INTEGER     Sequences shorter than minlen after truncation are Range(0, None)       discarded.                               [default: 1]" min="0" name="pminlen" optional="True" type="integer" value="1" />
    <param label="--p-maxns: INTEGER      Sequences with more than maxns N characters are Range(0, None)       discarded.                                 [optional]" name="pmaxns" optional="False" type="text" />
    <param label="--p-allowmergestagger: --p-allowmergestagger: / --p-no-allowmergestagger Allow joining of staggered read pairs. [default: False]" name="pallowmergestagger" selected="False" type="boolean" />
    <param label="--p-minovlen: INTEGER   Minimum overlap length of forward and reverse reads Range(0, None)       for joining.                            [default: 10]" min="0" name="pminovlen" optional="True" type="integer" value="10" />
    <param label="--p-maxdiffs: INTEGER   Maximum number of mismatches in the forward/reverse Range(0, None)       read overlap for joining.               [default: 10]" min="0" name="pmaxdiffs" optional="True" type="integer" value="10" />
    <param label="--p-minmergelen: INTEGER Range(0, None)       Minimum length of the joined read to be retained. [optional]" name="pminmergelen" optional="False" type="text" />
    <param label="--p-maxmergelen: INTEGER Range(0, None)       Maximum length of the joined read to be retained. [optional]" name="pmaxmergelen" optional="False" type="text" />
    <param label="--p-maxee: NUMBER       Maximum number of expected errors in the joined read Range(0.0, None)     to be retained.                            [optional]" name="pmaxee" optional="False" type="text" />
    <param exclude_max="False" label="--p-qmin: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score in the input. [default: 0]" max="2" min="-5" name="pqmin" optional="True" type="integer" value="0" />
    <param exclude_max="False" label="--p-qminout: INTEGER Range(-5, 2, inclusive_end=True) The minimum allowed quality score to use in output. [default: 0]" max="2" min="-5" name="pqminout" optional="True" type="integer" value="0" />
    <param exclude_max="False" label="--p-qmax: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score in the input. [default: 41]" max="41" min="40" name="pqmax" optional="True" type="integer" value="41" />
    <param exclude_max="False" label="--p-qmaxout: INTEGER Range(40, 41, inclusive_end=True) The maximum allowed quality score to use in output. [default: 41]" max="41" min="40" name="pqmaxout" optional="True" type="integer" value="41" />
    <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}: joinedsequences.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.
threads : Int % Range(0, 8, inclusive_end=True), optional
    The number of threads to use for computation. Does not scale much past
    4 threads.

Returns
-------
joined_sequences : SampleData[JoinedSequencesWithQuality]
    The joined sequences.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>