<?xml version="1.0" ?>
<tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2018.4">
	<description> - Demultiplex paired-end sequence data with barcodes in- sequence.</description>
	<requirements>
		<requirement type="package" version="2018.4">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-forward-barcodes-column="$mforwardbarcodescolumn"

  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
 
 --o-per-sample-sequences=opersamplesequences --o-untrimmed-sequences=ountrimmedsequences

  #if $perrorrate:
   --p-error-rate=$perrorrate
  #end if
  ;

  cp opersamplesequences.qza $opersamplesequences;
  cp ountrimmedsequences.qza $ountrimmedsequences;
  
]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-seqs: Multiplexed Paired End Barcode In Sequence - The paired-end sequences to be demultiplexed.  [required]" name="iseqs" optional="False" type="data"/>
		<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>
		<param label="--m-forward-barcodes-column: Metadata Column[Categorical] - Column from metadata file or artifact viewable as metadata. The sample metadata column listing the per-sample barcodes for the forward reads.  [required]" name="mforwardbarcodescolumn" optional="False" type="text"/>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
		<param label="--p-error-rate: The level of error tolerance, specified as the maximum allowable error rate.  [default: 0.1]" name="perrorrate" optional="True" type="float" value="0.1"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: per-sample-sequences.qza" name="opersamplesequences"/>
		<data format="qza" label="${tool.name} on ${on_string}: untrimmed-sequences.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.
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>
</tool>