diff qiime2/qiime_cutadapt_demux-single.xml @ 9:f190567fe3f6 draft

Uploaded

--- a/qiime2/qiime_cutadapt_demux-single.xml	Tue Aug 13 07:57:53 2019 -0400
+++ b/qiime2/qiime_cutadapt_demux-single.xml	Wed Aug 14 15:12:48 2019 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0" ?>
-<tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2019.4">
+<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="2019.4">qiime2</requirement>
+		<requirement type="package" version="2019.7">qiime2</requirement>
 	</requirements>
 	<command><![CDATA[
 qiime cutadapt demux-single
@@ -10,6 +10,30 @@
 --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 '__sq__' in str($mbarcodescolumn):
   #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
@@ -19,36 +43,25 @@
 --m-barcodes-column="$mbarcodescolumn"
 
 
---o-per-sample-sequences=opersamplesequences
---o-untrimmed-sequences=ountrimmedsequences
 
-
-
-
-
-
-#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 + ',' + d['additional_input'].__getattr__('file_name')
-#end for
-#return $file_list
-#end def
---m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+#if str($perrorrate):
+ --p-error-rate=$perrorrate
 #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 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" />
@@ -78,6 +91,15 @@
     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%).
+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.
 
 Returns
 -------