diff qiime2/qiime_dada2_denoise-paired.xml @ 9:f190567fe3f6 draft

Uploaded

--- a/qiime2/qiime_dada2_denoise-paired.xml	Tue Aug 13 07:57:53 2019 -0400
+++ b/qiime2/qiime_dada2_denoise-paired.xml	Wed Aug 14 15:12:48 2019 -0400
@@ -1,8 +1,8 @@
 <?xml version="1.0" ?>
-<tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired" version="2019.4">
+<tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired" version="2019.7">
 	<description> - Denoise and dereplicate paired-end sequences</description>
 	<requirements>
-		<requirement type="package" version="2019.4">qiime2</requirement>
+		<requirement type="package" version="2019.7">qiime2</requirement>
 	</requirements>
 	<command><![CDATA[
 
@@ -82,10 +82,20 @@
  --p-trim-left-r=$ptrimleftr
 #end if
 
-#if str($pmaxee):
- --p-max-ee=$pmaxee
+
+
+
+#if str($pmaxeef):
+ --p-max-ee-f=$pmaxeef
 #end if
 
+#if str($pmaxeer):
+ --p-max-ee-r=$pmaxeer
+#end if
+
+
+
+
 #if str($ptruncq):
  --p-trunc-q=$ptruncq
 #end if
@@ -130,7 +140,14 @@
 		<param label="--p-trunc-len-r: INTEGER Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 20 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenr" optional="False" value="" type="integer"/>
 		<param label="--p-trim-left-f: INTEGER Position at which forward read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles.      [default: 0]" name="ptrimleftf" optional="True" type="integer" value="0"/>
 		<param label="--p-trim-left-r: INTEGER Position at which reverse read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles.      [default: 0]" name="ptrimleftr" optional="True" type="integer" value="0"/>
-		<param label="--p-max-ee: NUMBER      Reads with number of expected errors higher than this value will be discarded.          [default: 2.0]" name="pmaxee" optional="True" type="float" value="2.0"/>
+
+
+
+		<param label="--p-max-ee-f: NUMBER      Forward reads with number of expected errors higher than this value will be discarded.     [default: 2.0]" name="pmaxeef" optional="True" type="float" value="2.0"/>
+		<param label="--p-max-ee-r: NUMBER      Reverse reads with number of expected errors higher than this value will be discarded.     [default: 2.0]" name="pmaxeer" optional="True" type="float" value="2.0"/>
+
+
+
 		<param label="--p-trunc-q: INTEGER    Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded.                   [default: 2]" name="ptruncq" optional="True" type="integer" value="2"/>
 		<param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
 			<option selected="True" value="None">Selection is Optional</option>
@@ -149,7 +166,7 @@
 	</outputs>
 	<help><![CDATA[
 Denoise and dereplicate paired-end sequences
-############################################
+#############################################
 
 This method denoises paired-end sequences, dereplicates them, and filters
 chimeras.
@@ -182,15 +199,18 @@
     Position at which reverse read sequences should be trimmed due to low
     quality. This trims the 5' end of the input sequences, which will be
     the bases that were sequenced in the first cycles.
-max_ee : Float, optional
-    Reads with number of expected errors higher than this value will be
-    discarded.
+max_ee_f : Float, optional
+    Forward reads with number of expected errors higher than this value
+    will be discarded.
+max_ee_r : Float, optional
+    Reverse reads with number of expected errors higher than this value
+    will be discarded.
 trunc_q : Int, optional
     Reads are truncated at the first instance of a quality score less than
     or equal to this value. If the resulting read is then shorter than
     `trunc_len_f` or `trunc_len_r` (depending on the direction of the read)
     it is discarded.
-chimera_method : Str % Choices('consensus', 'pooled', 'none'), optional
+chimera_method : Str % Choices('consensus', 'none', 'pooled'), optional
     The method used to remove chimeras. "none": No chimera removal is
     performed. "pooled": All reads are pooled prior to chimera detection.
     "consensus": Chimeras are detected in samples individually, and
@@ -202,7 +222,6 @@
     sequence being tested. Values should be greater than or equal to 1
     (i.e. parents should be more abundant than the sequence being tested).
     This parameter has no effect if chimera_method is "none".
-    provided, all available cores will be used.
 n_reads_learn : Int, optional
     The number of reads to use when training the error model. Smaller
     numbers will result in a shorter run time but a less reliable error