annotate qiime2/qiime_deblur_denoise-other.xml @ 15:276ec629f09a draft

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<?xml version="1.0" ?>
<tool id="qiime_deblur_denoise-other" name="qiime deblur denoise-other"
      version="2020.8">
  <description>Deblur sequences using a user-specified positive filter.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime deblur denoise-other

--i-demultiplexed-seqs=$idemultiplexedseqs

--i-reference-seqs=$ireferenceseqs

--p-trim-length=$ptrimlength

--p-left-trim-len=$plefttrimlen

#if $psamplestats:
 --p-sample-stats
#end if

--p-mean-error=$pmeanerror

--p-indel-prob=$pindelprob

--p-indel-max=$pindelmax

--p-min-reads=$pminreads

--p-min-size=$pminsize

--p-jobs-to-start=$pjobstostart

#if $pnohashedfeatureids:
 --p-no-hashed-feature-ids
#end if

--o-table=otable

--o-representative-sequences=orepresentativesequences

--o-stats=ostats

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp ostats.qza $ostats

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-reference-seqs: ARTIFACT FeatureData[Sequence] Positive filtering database. Keep all sequences aligning to these sequences.               [required]" name="ireferenceseqs" optional="False" type="data" />
    <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming.                                  [required]" name="ptrimlength" optional="False" type="text" />
    <param label="--p-left-trim-len: INTEGER Range(0, None)       Sequence trimming from the 5\' end. A value of 0 will disable this trim.                       [default: 0]" min="0" name="plefttrimlen" optional="True" type="integer" value="0" />
    <param label="--p-sample-stats: --p-sample-stats: / --p-no-sample-stats If true, gather stats per sample.    [default: False]" name="psamplestats" selected="False" type="boolean" />
    <param label="--p-mean-error: NUMBER  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: NUMBER  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: INTEGER  Maximum number of insertion/deletions.   [default: 3]" name="pindelmax" optional="True" type="integer" value="3" />
    <param label="--p-min-reads: INTEGER  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: INTEGER   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-no-hashed-feature-ids: Do not if true, hash the feature IDs.        [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
    <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
    <data format="qza" label="${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[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
    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.
left_trim_len : Int % Range(0, None), optional
    Sequence trimming from the 5' end. A value of 0 will disable this trim.
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>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>