<?xml version="1.0" ?>
<tool id="qiime_feature-classifier_extract-reads" name="qiime feature-classifier extract-reads" version="2018.4">
	<description> - Extract reads from reference</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  qiime feature-classifier extract-reads --i-sequences=$isequences --p-r-primer="$prprimer" --p-f-primer="$pfprimer"
  
  #if $ptrunclen:
   --p-trunc-len=$ptrunclen
  #end if
  
  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
  
  #if $ptrimleft:
   --p-trim-left=$ptrimleft
  #end if
   --o-reads=oreads
  #if $pidentity:
   --p-identity=$pidentity
  #end if
  ;
  cp oreads.qza $oreads;
  ]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] [required]" name="isequences" optional="False" type="data"/>
		<param label="--p-f-primer: forward primer sequence  [required]" name="pfprimer" optional="False" type="text"/>
		<param label="--p-r-primer: reverse primer sequence  [required]" name="prprimer" optional="False" type="text"/>
		<param label="--p-trunc-len: read is cut to trunc_len if trunc_len is positive. Applied before trim_left. [default: 0]" name="ptrunclen" optional="True" type="integer" value="0"/>
		<param label="--p-trim-left: trim_left nucleotides are removed from the 5' end if trim_left is positive. Applied after trunc_len.  [default: 0]" name="ptrimleft" optional="True" type="integer" value="0"/>
		<param label="--p-identity: minimum combined primer match identity threshold.  [default: 0.8]" name="pidentity" optional="True" type="float" value="0.8"/>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: reads.qza" name="oreads"/>
	</outputs>
	<help><![CDATA[
Extract reads from reference
-----------------------------

Extract sequencing-like reads from a reference database.

Parameters
----------
sequences : FeatureData[Sequence]

f_primer : Str
    forward primer sequence
r_primer : Str
    reverse primer sequence
trunc_len : Int, optional
    read is cut to trunc_len if trunc_len is positive. Applied 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.
identity : Float, optional
    minimum combined primer match identity threshold.

Returns
-------
reads : FeatureData[Sequence]
]]>
	</help>
<macros>
	<import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation" />
</tool>