--- a/qiime2/qiime_cutadapt_demux-single.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_cutadapt_demux-single.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,80 +1,85 @@
 <?xml version="1.0" ?>
-<tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2019.7">
-	<description> - Demultiplex single-end sequence data with barcodes in- sequence.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single"
+      version="2020.8">
+  <description>Demultiplex single-end sequence data with barcodes in- sequence.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime cutadapt demux-single
 
 --i-seqs=$iseqs
-
-
-#if str($pbatchsize):
-  --p-batch-size $pbatchsize
-#end if
-
-#if str($pminimumlength):
-  --p-minimum-length $pminimumlength
-#end if
-
-
-
-
+# if $input_files_mbarcodesfile:
+  # 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-barcodes-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+# end if
 
-#if $input_files_mbarcodesfile:
-#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-barcodes-file=' + d['additional_input'].__getattr__('file_name')
-#end for
-#return $file_list
-#end def
---m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+#if '__ob__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
 #end if
-
-
-
+#if '__cb__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
+#if 'X' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
 #if '__sq__' in str($mbarcodescolumn):
   #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
   #set $mbarcodescolumn = $mbarcodescolumn_temp
 #end if
+#if '__db__' in str($mbarcodescolumn):
+  #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
+  #set $mbarcodescolumn = $mbarcodescolumn_temp
+#end if
 
---m-barcodes-column="$mbarcodescolumn"
-
+--m-barcodes-column=$mbarcodescolumn
 
 
-#if str($perrorrate):
- --p-error-rate=$perrorrate
-#end if
+--p-error-rate=$perrorrate
 
+--p-minimum-length=$pminimumlength
 
 --o-per-sample-sequences=opersamplesequences
+
 --o-untrimmed-sequences=ountrimmedsequences
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-
-cp opersamplesequences.qza $opersamplesequences;
 cp ountrimmedsequences.qza $ountrimmedsequences
-	]]></command>
-	<inputs>
-
-		<param label="--p-batch-size:  INTEGER  The number of samples cutadapt demultiplexes Range(0, None) 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. [default: 0]" name="pbatchsize" optional="True" type="integer" value="0" min="0"/>
-		<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]" name="pminimumlength" optional="True" type="integer" value="1" min="1"/>
-
 
-		<param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
-		<repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
-			<param label="--m-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-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes.                                 [required]" name="mbarcodescolumn" optional="False" type="text"/>
-		<param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [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 ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
-	</outputs>
-	<help><![CDATA[
-Demultiplex single-end sequence data with barcodes in-sequence.
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
+    <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--m-barcodes-column: COLUMN  MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes.                                 [required]" name="mbarcodescolumn" optional="False" type="text" />
+    <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
+    <param label="--p-minimum-length: INTEGER Range(1, None)        Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${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 single-end sequence data with barcodes in- sequence.
 ###############################################################
 
 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
@@ -107,9 +112,9 @@
     The resulting demultiplexed sequences.
 untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
     The sequences that were unmatched to barcodes.
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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