view qiime2-2020.8/qiime_quality-control_filter-reads.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_quality-control_filter-reads" name="qiime quality-control filter-reads"
      version="2020.8">
  <description>Filter demultiplexed sequences by alignment to reference database.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime quality-control filter-reads

--i-demultiplexed-sequences=$idemultiplexedsequences

--i-database=$idatabase

--p-n-threads=$pnthreads

#if str($pmode) != 'None':
--p-mode=$pmode
#end if

#if str($psensitivity) != 'None':
--p-sensitivity=$psensitivity
#end if

--p-ref-gap-open-penalty=$prefgapopenpenalty

--p-ref-gap-ext-penalty=$prefgapextpenalty

#if $pnoexcludeseqs:
 --p-no-exclude-seqs
#end if

--o-filtered-sequences=ofilteredsequences

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

;
cp ofilteredsequences.qza $ofilteredsequences

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²] The sequences to be trimmed.               [required]" name="idemultiplexedsequences" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-database: ARTIFACT  Bowtie2 indexed database. Bowtie2Index                                                    [required]" name="idatabase" optional="False" type="data" />
    <param label="--p-mode: " name="pmode" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="local">local</option>
      <option value="global">global</option>
    </param>
    <param label="--p-sensitivity: " name="psensitivity" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="very-fast">very-fast</option>
      <option value="fast">fast</option>
      <option value="sensitive">sensitive</option>
      <option value="very-sensitive">very-sensitive</option>
    </param>
    <param label="--p-ref-gap-open-penalty: INTEGER Range(1, None)       Reference gap open penalty.              [default: 5]" min="1" name="prefgapopenpenalty" optional="True" type="integer" value="5" />
    <param label="--p-ref-gap-ext-penalty: INTEGER Range(1, None)       Reference gap extend penalty.            [default: 3]" min="1" name="prefgapextpenalty" optional="True" type="integer" value="3" />
    <param label="--p-no-exclude-seqs: Do not exclude sequences that align to reference. Set this option to False to exclude sequences that do not align to the reference database.      [default: True]" name="pnoexcludeseqs" 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}: filteredsequences.qza" name="ofilteredsequences" />
    
  </outputs>

  <help><![CDATA[
Filter demultiplexed sequences by alignment to reference database.
###############################################################

Filter out (or keep) demultiplexed single- or paired-end sequences that
align to a reference database, using bowtie2 and samtools. This method can
be used to filter out human DNA sequences and other contaminants in any
FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or
alternatively (when exclude_seqs is False) to only keep sequences that do
align to the reference.

Parameters
----------
demultiplexed_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
    The sequences to be trimmed.
database : Bowtie2Index
    Bowtie2 indexed database.
n_threads : Int % Range(1, None), optional
    Number of alignment threads to launch.
mode : Str % Choices('local', 'global'), optional
    Bowtie2 alignment settings. See bowtie2 manual for more details.
sensitivity : Str % Choices('very-fast', 'fast', 'sensitive', 'very-sensitive'), optional
    Bowtie2 alignment sensitivity. See bowtie2 manual for details.
ref_gap_open_penalty : Int % Range(1, None), optional
    Reference gap open penalty.
ref_gap_ext_penalty : Int % Range(1, None), optional
    Reference gap extend penalty.
exclude_seqs : Bool, optional
    Exclude sequences that align to reference. Set this option to False to
    exclude sequences that do not align to the reference database.

Returns
-------
filtered_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
    The resulting filtered sequences.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>