<?xml version="1.0" ?>
<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=$isequences

--p-f-primer=$pfprimer

--p-r-primer=$prprimer

--p-trim-right=$ptrimright

--p-trunc-len=$ptrunclen

--p-trim-left=$ptrimleft

--p-identity=$pidentity

--p-min-length=$pminlength

--p-max-length=$pmaxlength

--p-n-jobs=$pnjobs

#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>
    <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>

  <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 (5' -> 3').
r_primer : Str
    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 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 trim_right and trunc_len.
identity : Float, optional
    minimum combined primer match identity threshold.
min_length : Int % Range(0, None), optional
    Minimum amplicon length. Shorter amplicons are discarded. Applied after
    trimming and truncation, so be aware that trimming may impact sequence
    retention. Set to zero to disable min length filtering.
max_length : Int % Range(0, None), optional
    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>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>