--- a/qiime2/qiime_feature-classifier_extract-reads.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_feature-classifier_extract-reads.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,100 +1,104 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2019.7">
-	<description> - Extract reads from reference</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
-
-
-#if str( $input_sequences.selector ) == 'history'
-	#set $seq = $input_sequences.i_sequences
-
-#else:
-	qiime tools import --type 'FeatureData[Sequence]' --input-path '$input_sequences.i_sequences.fields.path' --output-path database.qza;
-	#set $seq = 'database.qza'
-#end if
-
-
+<tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads"
+      version="2020.8">
+  <description>Extract reads from reference sequences.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime feature-classifier extract-reads
 
---i-sequences=$seq
+--i-sequences=$isequences
+
+--p-f-primer=$pfprimer
 
---p-f-primer="$pfprimer"
---p-r-primer="$prprimer"
+--p-r-primer=$prprimer
 
-#if str($ptrunclen):
- --p-trunc-len=$ptrunclen
-#end if
+--p-trim-right=$ptrimright
+
+--p-trunc-len=$ptrunclen
 
-#if str($ptrimleft):
- --p-trim-left=$ptrimleft
-#end if
+--p-trim-left=$ptrimleft
+
+--p-identity=$pidentity
+
+--p-min-length=$pminlength
 
-#if str($pidentity):
- --p-identity=$pidentity
-#end if
+--p-max-length=$pmaxlength
 
-#if str($pminlength):
- --p-min-length=$pminlength
-#end if
+--p-n-jobs=$pnjobs
 
-#if str($pmaxlength):
- --p-max-length=$pmaxlength
+#if str($preadorientation) != 'None':
+--p-read-orientation=$preadorientation
 #end if
 
 --o-reads=oreads
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
 cp oreads.qza $oreads
-	]]></command>
-	<inputs>
-		<conditional name="input_sequences" optional="False">
-		   <param name="selector" type="select" label="--i-sequences: FeatureData[Sequence] [required] - Reference sequences to query">
-			  <option value="cached">Public databases</option>
-			  <option value="history">Databases from your history</option>
-		   </param>
-		   <when value="cached">
-			  <param name="i_sequences" label="--i-sequences: FeatureData[Sequence] [required] - Reference sequences" type="select" optional="True">
-				 <options from_data_table="qiime_rep_set" />
-			  </param>
-		   </when>
-		   <when value="history">
-			  <param name="i_sequences" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
-		   </when>
-		</conditional>
 
-		<param label="--p-f-primer: TEXT       forward primer sequence                   [required]" name="pfprimer" optional="False" type="text"/>
-		<param label="--p-r-primer: TEXT       reverse primer sequence                   [required]" name="prprimer" optional="False" type="text"/>
-		<param label="--p-trunc-len: INTEGER   read is cut to trunc-len if trunc-len is positive. Applied before trim-left.               [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/>
-		<param label="--p-trim-left: INTEGER   trim-left nucleotides are removed from the 5' end if trim-left is positive. Applied after trunc-len. [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
-		<param label="--p-identity: NUMBER     minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>
-		<param label="--p-min-length: INTEGER  Minimum amplicon length. Shorter amplicons are Range(0, None)        discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering.                             [default: 50]" name="pminlength" optional="True" type="integer" min="0" value="50"/>
-		<param label="--p-max-length: INTEGER  Maximum amplicon length. Longer amplicons are Range(0, None)        discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering.           [default: 0]" name="pmaxlength" optional="True" type="integer" min="0" value="0"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads"/>
-	</outputs>
-	<help><![CDATA[
-Extract reads from reference
-############################
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] [required]" name="isequences" optional="False" type="data" />
+    <param label="--p-f-primer: TEXT       forward primer sequence (5\' -&gt; 3\').       [required]" name="pfprimer" optional="False" type="text" />
+    <param label="--p-r-primer: TEXT       reverse primer sequence (5\' -&gt; 3\'). Do not use reverse-complemented primer sequence.     [required]" name="prprimer" optional="False" type="text" />
+    <param label="--p-trim-right: INTEGER  trim-right nucleotides are removed from the 3\' end if trim-right is positive. Applied before trunc-len and trim-left.                          [default: 0]" name="ptrimright" optional="True" type="integer" value="0" />
+    <param label="--p-trunc-len: INTEGER   read is cut to trunc-len if trunc-len is positive. Applied after trim-right but before trim-left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0" />
+    <param label="--p-trim-left: INTEGER   trim-left nucleotides are removed from the 5\' end if trim-left is positive. Applied after trim-right and trunc-len.                          [default: 0]" name="ptrimleft" optional="True" type="integer" value="0" />
+    <param label="--p-identity: NUMBER     minimum combined primer match identity threshold. [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8" />
+    <param label="--p-min-length: INTEGER  Minimum amplicon length. Shorter amplicons are Range(0, None)        discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering.                             [default: 50]" min="0" name="pminlength" optional="True" type="integer" value="50" />
+    <param label="--p-max-length: INTEGER  Maximum amplicon length. Longer amplicons are Range(0, None)        discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering.           [default: 0]" min="0" name="pmaxlength" optional="True" type="integer" value="0" />
+    <param label="--p-read-orientation: " name="preadorientation" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="both">both</option>
+      <option value="forward">forward</option>
+      <option value="reverse">reverse</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-Extract sequencing-like reads from a reference database.
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Extract reads from reference sequences.
+###############################################################
+
+Extract simulated amplicon reads from a reference database. Performs in-
+silico PCR to extract simulated amplicons from reference sequences that
+match the input primer sequences (within the mismatch threshold specified
+by `identity`). Both primer sequences must be in the 5' -> 3' orientation.
+Sequences that fail to match both primers will be excluded. Reads are
+extracted, trimmed, and filtered in the following order: 1. reads are
+extracted in specified orientation; 2. primers are removed; 3. reads longer
+than `max_length` are removed; 4. reads are trimmed with `trim_right`; 5.
+reads are truncated to `trunc_len`; 6. reads are trimmed with `trim_left`;
+7. reads shorter than `min_length` are removed.
 
 Parameters
 ----------
 sequences : FeatureData[Sequence]
-	\
-
 f_primer : Str
-    forward primer sequence
+    forward primer sequence (5' -> 3').
 r_primer : Str
-    reverse primer sequence
+    reverse primer sequence (5' -> 3'). Do not use reverse-complemented
+    primer sequence.
+trim_right : Int, optional
+    trim_right nucleotides are removed from the 3' end if trim_right is
+    positive. Applied before trunc_len and trim_left.
 trunc_len : Int, optional
-    read is cut to trunc_len if trunc_len is positive. Applied before
-    trim_left.
+    read is cut to trunc_len if trunc_len is positive. Applied after
+    trim_right but before trim_left.
 trim_left : Int, optional
     trim_left nucleotides are removed from the 5' end if trim_left is
-    positive. Applied after trunc_len.
+    positive. Applied after trim_right and trunc_len.
 identity : Float, optional
     minimum combined primer match identity threshold.
 min_length : Int % Range(0, None), optional
@@ -105,13 +109,22 @@
     Maximum amplicon length. Longer amplicons are discarded. Applied before
     trimming and truncation, so plan accordingly. Set to zero (default) to
     disable max length filtering.
+n_jobs : Int % Range(1, None), optional
+    Number of seperate processes to run.
+batch_size : Int % Range(1, None) | Str % Choices('auto'), optional
+    Number of sequences to process in a batch. The `auto` option is
+    calculated from the number of sequences and number of jobs specified.
+read_orientation : Str % Choices('both', 'forward', 'reverse'), optional
+    Orientation of primers relative to the sequences: "forward" searches
+    for primer hits in the forward direction, "reverse" searches reverse-
+    complement, and "both" searches both directions.
 
 Returns
 -------
 reads : FeatureData[Sequence]
-	]]></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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