--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_cutadapt_demux-paired.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,170 @@
+<?xml version="1.0" ?>
+<tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired"
+      version="2020.8">
+  <description>Demultiplex paired-end sequence data with barcodes in- sequence.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime cutadapt demux-paired
+
+--i-seqs=$iseqs
+# if $input_files_mforwardbarcodesfile:
+  # 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 + ' --m-forward-barcodes-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-forward-barcodes-file=$list_dict_to_string($input_files_mforwardbarcodesfile)
+# end if
+
+#if '__ob__' in str($mforwardbarcodescolumn):
+  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__ob__', '[')
+  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
+#end if
+#if '__cb__' in str($mforwardbarcodescolumn):
+  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__cb__', ']')
+  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
+#end if
+#if 'X' in str($mforwardbarcodescolumn):
+  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('X', '\\')
+  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
+#end if
+#if '__sq__' in str($mforwardbarcodescolumn):
+  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'")
+  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
+#end if
+#if '__db__' in str($mforwardbarcodescolumn):
+  #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
+  #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
+#end if
+
+--m-forward-barcodes-column=$mforwardbarcodescolumn
+
+# if $input_files_mreversebarcodesfile:
+  # 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 + ' --m-reverse-barcodes-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-reverse-barcodes-file=$list_dict_to_string($input_files_mreversebarcodesfile)
+# end if
+
+#if '__ob__' in str($mreversebarcodescolumn):
+  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__ob__', '[')
+  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
+#end if
+#if '__cb__' in str($mreversebarcodescolumn):
+  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__cb__', ']')
+  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
+#end if
+#if 'X' in str($mreversebarcodescolumn):
+  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('X', '\\')
+  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
+#end if
+#if '__sq__' in str($mreversebarcodescolumn):
+  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'")
+  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
+#end if
+#if '__db__' in str($mreversebarcodescolumn):
+  #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"')
+  #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
+#end if
+
+#if str($mreversebarcodescolumn):
+  --m-reverse-barcodes-column=$mreversebarcodescolumn
+#end if
+
+--p-error-rate=$perrorrate
+
+--p-minimum-length=$pminimumlength
+
+#if $pmixedorientation:
+ --p-mixed-orientation
+#end if
+
+--o-per-sample-sequences=opersamplesequences
+
+--o-untrimmed-sequences=ountrimmedsequences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+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" />
+    <repeat name="input_files_mforwardbarcodesfile" optional="True" title="--m-forward-barcodes-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-forward-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <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" />
+    <repeat name="input_files_mreversebarcodesfile" optional="True" title="--m-reverse-barcodes-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-reverse-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <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="False" type="text" />
+    <param exclude_max="False" 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]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
+    <param label="--p-minimum-length: INTEGER Range(1, None)        Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
+    <param label="--p-mixed-orientation: --p-mixed-orientation: / --p-no-mixed-orientation Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file).                         [default: False]" name="pmixedorientation" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
+    <data format="qza" label="${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.
+batch_size : Int % Range(0, None), optional
+    The number of samples cutadapt demultiplexes concurrently.
+    Demultiplexing in smaller batches will yield the same result with
+    marginal speed loss, and may solve "too many files" errors related to
+    sample quantity. Set to "0" to process all samples at once.
+minimum_length : Int % Range(1, None), optional
+    Discard reads shorter than specified value. Note, the cutadapt default
+    of 0 has been overridden, because that value produces empty sequence
+    records.
+mixed_orientation : Bool, optional
+    Handle demultiplexing of mixed orientation reads (i.e. when forward and
+    reverse reads coexist in the same file).
+
+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>
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