<?xml version="1.0" ?>
<tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other" version="2018.4">
	<description> - Deblur sequences using a user-specified positive filter.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
  qiime deblur denoise-other --i-demultiplexed-seqs=$idemultiplexedseqs --p-trim-length="$ptrimlength" --i-reference-seqs=$ireferenceseqs

  #if str($cmdconfig) != 'None':
   --cmd-config=$cmdconfig
  #end if
  
  #if $phashedfeatureids:
   --p-hashed-feature-ids
  #else 
  --p-no-hashed-feature-ids
  #end if
  
  #if $pindelprob:
   --p-indel-prob=$pindelprob
  #end if
  
  #if $pindelmax:
   --p-indel-max=$pindelmax
  #end if
  
  #if $pmeanerror:
   --p-mean-error=$pmeanerror
  #end if
  
   --o-representative-sequences=orepresentativesequences --o-table=otable --o-stats=ostats
   
  #set $pjobstostart = '${GALAXY_SLOTS:-4}'
  
  #if str($pjobstostart):
   --p-jobs-to-start="$pjobstostart"
  #end if  
  
  #if $pminreads:
   --p-min-reads=$pminreads
  #end if
  
  #if $pminsize:
   --p-min-size=$pminsize
  #end if  
  
   --p-sample-stats  
  ;
  cp orepresentativesequences.qza $orepresentativesequences;
  cp otable.qza $otable;
  cp ostats.qza $ostats;
  ]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
		<param format="qza,no_unzip.zip" label="--i-reference-seqs: FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences. [required]" name="ireferenceseqs" optional="False" type="data"/>
		<param label="--p-trim-length: Sequence trim length, specify -1 to disable trimming.  [required]" name="ptrimlength" optional="False" type="text"/>		
		<param label="--p-mean-error: The mean per nucleotide error, used for original sequence estimate.  [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005"/>
		<param label="--p-indel-prob: Insertion/deletion (indel) probability (same for N indels).  [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01"/>
		<param label="--p-indel-max: Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3"/>
		<param label="--p-min-reads: Retain only features appearing at least min_reads times across all samples in the resulting feature table.  [default: 10]" name="pminreads" optional="True" type="integer" value="10"/>
		<param label="--p-min-size: In each sample, discard all features with an abundance less than min_size.  [default: 2]" name="pminsize" optional="True" type="integer" value="2"/>
		<param label="--p-hashed-feature-ids: --p-no-hashed-feature-ids If true, hash the feature IDs.  [default: True]" name="phashedfeatureids" checked="True" type="boolean"/>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: representative-sequences.qza" name="orepresentativesequences"/>
		<data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
		<data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
	</outputs>
	<help><![CDATA[
Deblur sequences using a user-specified positive filter.
---------------------------------------------------------

Perform sequence quality control for Illumina data using the Deblur
workflow, including positive alignment-based filtering. Only forward reads
are supported at this time. This mode of execution is particularly useful
when operating on non-16S data. For example, to apply Deblur to 18S data,
you would want to specify a reference composed of 18S sequences in order to
filter out sequences which do not appear to be 18S. The assessment is
performed by local alignment using SortMeRNA with a permissive e-value
threshold.

Parameters
----------
demultiplexed_seqs : SampleData[JoinedSequencesWithQuality | PairedEndSequencesWithQuality | SequencesWithQuality]
    The demultiplexed sequences to be denoised.
reference_seqs : FeatureData[Sequence]
    Positive filtering database. Keep all sequences aligning to these
    sequences.
trim_length : Int
    Sequence trim length, specify -1 to disable trimming.
sample_stats : Bool, optional
    If true, gather stats per sample.
mean_error : Float, optional
    The mean per nucleotide error, used for original sequence estimate.
indel_prob : Float, optional
    Insertion/deletion (indel) probability (same for N indels).
indel_max : Int, optional
    Maximum number of insertion/deletions.
min_reads : Int, optional
    Retain only features appearing at least min_reads times across all
    samples in the resulting feature table.
min_size : Int, optional
    In each sample, discard all features with an abundance less than
    min_size.
jobs_to_start : Int, optional
    Number of jobs to start (if to run in parallel).
hashed_feature_ids : Bool, optional
    If true, hash the feature IDs.

Returns
-------
table : FeatureTable[Frequency]
    The resulting denoised feature table.
representative_sequences : FeatureData[Sequence]
    The resulting feature sequences.
stats : DeblurStats
    Per-sample stats if requested.
      ]]>
	</help>
</tool>