--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_demux-paired.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,92 @@
+<?xml version="1.0" ?>
+<tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2019.4">
+	<description> - Demultiplex paired-end sequence data with barcodes in- sequence.</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime cutadapt demux-paired
+--i-seqs=$iseqs
+
+#def list_dict_to_string(list_dict):
+  #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+  #for d in list_dict[1:]:
+	  #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+  #end for
+  #return $file_list
+#end def
+
+--m-forward-barcodes-file=$list_dict_to_string("$input_files_mforwardbarcodesfile")
+--m-reverse-barcodes-file=$list_dict_to_string("$input_files_mreversebarcodesfile")
+
+--m-forward-barcodes-column="$mforwardbarcodescolumn"
+
+#if str($mreversebarcodescolumn):
+ --m-reverse-barcodes-column="$mreversebarcodescolumn"
+#end if
+
+#if $perrorrate:
+ --p-error-rate=$perrorrate
+#end if
+
+
+--o-per-sample-sequences=opersamplesequences
+--o-untrimmed-sequences=ountrimmedsequences
+;
+
+cp opersamplesequences.qza $opersamplesequences;
+cp ountrimmedsequences.qza $ountrimmedsequences
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedPairedEndBarcodeInSequence The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
+		<param label="--m-forward-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the forward reads.           [required]" name="mforwardbarcodescolumn" optional="False" type="text"/>
+		<param label="--m-reverse-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the reverse reads.           [optional]" name="mreversebarcodescolumn" optional="True" type="text"/>
+
+		<repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
+			<param label="--m-forward-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+
+		<repeat name="input_files_mreversebarcodesfile" optional="False" title="--m-reverse-barcodes-file">
+			<param label="--m-reverse-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+
+		<param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate.         [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
+		<data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
+	</outputs>
+	<help><![CDATA[
+Demultiplex paired-end sequence data with barcodes in-sequence.
+###############################################################
+
+Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
+are expected to be located within the sequence data (versus the header, or
+a separate barcode file).
+
+Parameters
+----------
+seqs : MultiplexedPairedEndBarcodeInSequence
+    The paired-end sequences to be demultiplexed.
+forward_barcodes : MetadataColumn[Categorical]
+    The sample metadata column listing the per-sample barcodes for the
+    forward reads.
+reverse_barcodes : MetadataColumn[Categorical], optional
+    The sample metadata column listing the per-sample barcodes for the
+    reverse reads.
+error_rate : Float % Range(0, 1, inclusive_end=True), optional
+    The level of error tolerance, specified as the maximum allowable error
+    rate.
+
+Returns
+-------
+per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
+    The resulting demultiplexed sequences.
+untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
+    The sequences that were unmatched to barcodes.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>