comparison qiime2-2020.8/qiime_feature-classifier_classify-consensus-blast.xml @ 20:d93d8888f0b0 draft

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20:d93d8888f0b0

<?xml version="1.0" ?>
<tool id="qiime_feature-classifier_classify-consensus-blast" name="qiime feature-classifier classify-consensus-blast"
      version="2020.8">
  <description>BLAST+ consensus taxonomy classifier</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime feature-classifier classify-consensus-blast

--i-query=$iquery

--i-reference-reads=$ireferencereads

--i-reference-taxonomy=$ireferencetaxonomy

--p-maxaccepts=$pmaxaccepts

--p-perc-identity=$ppercidentity

--p-query-cov=$pquerycov

#if str($pstrand) != 'None':
--p-strand=$pstrand
#end if

--p-evalue=$pevalue

--p-min-consensus=$pminconsensus

#if str($punassignablelabel):
  --p-unassignable-label=$punassignablelabel
#end if
--o-classification=oclassification

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

;
cp oclassification.qza $oclassification

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-query: ARTIFACT FeatureData[Sequence] Sequences to classify taxonomically.      [required]" name="iquery" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-reference-reads: ARTIFACT FeatureData[Sequence] reference sequences.                      [required]" name="ireferencereads" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] reference taxonomy labels.                [required]" name="ireferencetaxonomy" optional="False" type="data" />
    <param label="--p-maxaccepts: INTEGER  Maximum number of hits to keep for each query. Must Range(1, None)        be in range [1, infinity]. BLAST will choose the first N hits in the reference database that exceed perc-identity similarity to query.     [default: 10]" min="1" name="pmaxaccepts" optional="True" type="integer" value="10" />
    <param exclude_max="False" label="--p-perc-identity: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if percent identity to query is lower. Must be in range [0.0, 1.0].          [default: 0.8]" max="1.0" min="0.0" name="ppercidentity" optional="True" type="float" value="0.8" />
    <param exclude_max="False" label="--p-query-cov: PROPORTION Range(0.0, 1.0, inclusive_end=True) Reject match if query alignment coverage per high-scoring pair is lower. Note: this uses blastn\'s qcov_hsp_perc parameter, and may not behave identically to the query-cov parameter used by classify-consensus-vsearch. Must be in range [0.0, 1.0].                                 [default: 0.8]" max="1.0" min="0.0" name="pquerycov" optional="True" type="float" value="0.8" />
    <param label="--p-strand: " name="pstrand" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="both">both</option>
      <option value="plus">plus</option>
      <option value="minus">minus</option>
    </param>
    <param label="--p-evalue: NUMBER       BLAST expectation value (E) threshold for saving hits.                               [default: 0.001]" name="pevalue" optional="True" type="float" value="0.001" />
    <param exclude_max="False" exclude_min="True" label="--p-min-consensus: NUMBER Range(0.5, 1.0, inclusive_start=False, inclusive_end=True)   Minimum fraction of assignments must match top hit to be accepted as consensus assignment. Must be in range (0.5, 1.0].                    [default: 0.51]" max="1.0" min="0.5" name="pminconsensus" optional="True" type="float" value="0.51" />
    <param label="--p-unassignable-label: TEXT [default: \'Unassigned\']" name="punassignablelabel" optional="False" type="text" value="\'Unassigned\'" />
    <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}: classification.qza" name="oclassification" />
    
  </outputs>

  <help><![CDATA[
BLAST+ consensus taxonomy classifier
###############################################################

Assign taxonomy to query sequences using BLAST+. Performs BLAST+ local
alignment between query and reference_reads, then assigns consensus
taxonomy to each query sequence from among maxaccepts hits, min_consensus
of which share that taxonomic assignment. Note that maxaccepts selects the
first N hits with > perc_identity similarity to query, not the top N
matches. For top N hits, use classify-consensus-vsearch.

Parameters
----------
query : FeatureData[Sequence]
    Sequences to classify taxonomically.
reference_reads : FeatureData[Sequence]
    reference sequences.
reference_taxonomy : FeatureData[Taxonomy]
    reference taxonomy labels.
maxaccepts : Int % Range(1, None), optional
    Maximum number of hits to keep for each query. Must be in range [1,
    infinity]. BLAST will choose the first N hits in the reference database
    that exceed perc_identity similarity to query.
perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Reject match if percent identity to query is lower. Must be in range
    [0.0, 1.0].
query_cov : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Reject match if query alignment coverage per high-scoring pair is
    lower. Note: this uses blastn's qcov_hsp_perc parameter, and may not
    behave identically to the query_cov parameter used by classify-
    consensus-vsearch. Must be in range [0.0, 1.0].
strand : Str % Choices('both', 'plus', 'minus'), optional
    Align against reference sequences in forward ("plus"), reverse
    ("minus"), or both directions ("both").
evalue : Float, optional
    BLAST expectation value (E) threshold for saving hits.
min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
    Minimum fraction of assignments must match top hit to be accepted as
    consensus assignment. Must be in range (0.5, 1.0].
unassignable_label : Str, optional

Returns
-------
classification : FeatureData[Taxonomy]
    Taxonomy classifications of query sequences.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>