--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_vsearch_join-pairs.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,137 @@
+<?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>
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