view qiime2/qiime_quality-control_evaluate-taxonomy.xml @ 15:276ec629f09a draft

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<?xml version="1.0" ?>
<tool id="qiime_quality-control_evaluate-taxonomy" name="qiime quality-control evaluate-taxonomy"
      version="2020.8">
  <description>Evaluate expected vs. observed taxonomic assignments</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime quality-control evaluate-taxonomy

--i-expected-taxa=$iexpectedtaxa

--i-observed-taxa=$iobservedtaxa

#if $ifeaturetable:
 --i-feature-table
#end if

--p-depth=$pdepth

#if str($ppalette) != 'None':
--p-palette=$ppalette
#end if

#if $pnorequireexpids:
 --p-no-require-exp-ids
#end if

#if $pnorequireobsids:
 --p-no-require-obs-ids
#end if

#if str($psampleid):
  --p-sample-id=$psampleid
#end if
--o-visualization=ovisualization

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

;
cp odatabase.qza $odatabase

;
qiime tools export  ovisualization.qzv --output-path out
&& mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization'

;
qiime tools export  ovisualization.qzv --output-path out
&& mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization'

;
qiime tools export  ovisualization.qzv --output-path out
&& mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization'

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-expected-taxa: ARTIFACT FeatureData[Taxonomy] Expected taxonomic assignments               [required]" name="iexpectedtaxa" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-observed-taxa: ARTIFACT FeatureData[Taxonomy] Observed taxonomic assignments               [required]" name="iobservedtaxa" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-feature-table: --i-feature-table: ARTIFACT FeatureTable[RelativeFrequency] Optional feature table containing relative frequency of each feature, used to weight accuracy scores by frequency. Must contain all features found in expected and/or observed taxa. Features found in the table but not the expected/observed taxa will be dropped prior to analysis.                                    [optional]" name="ifeaturetable" selected="False" type="boolean" />
    <param label="--p-depth: INTEGER    Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database).                [required]" name="pdepth" optional="False" type="text" />
    <param label="--p-palette: " name="ppalette" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Set1">Set1</option>
      <option value="Set2">Set2</option>
      <option value="Set3">Set3</option>
      <option value="Pastel1">Pastel1</option>
      <option value="Pastel2">Pastel2</option>
      <option value="Paired">Paired</option>
      <option value="Accent">Accent</option>
      <option value="Dark2">Dark2</option>
      <option value="tab10">tab10</option>
      <option value="tab20">tab20</option>
      <option value="tab20b">tab20b</option>
      <option value="tab20c">tab20c</option>
      <option value="viridis">viridis</option>
      <option value="plasma">plasma</option>
      <option value="inferno">inferno</option>
      <option value="magma">magma</option>
      <option value="terrain">terrain</option>
      <option value="rainbow">rainbow</option>
    </param>
    <param label="--p-no-require-exp-ids: Do not require that all features found in observed taxa must be found in expected taxa or raise error. [default: True]" name="pnorequireexpids" selected="False" type="boolean" />
    <param label="--p-no-require-obs-ids: Do not require that all features found in expected taxa must be found in observed taxa or raise error. [default: True]" name="pnorequireobsids" selected="False" type="boolean" />
    <param label="--p-sample-id: TEXT   Optional sample ID to use for extracting frequency data from feature table, and for labeling accuracy results. If no sample-id is provided, feature frequencies are derived from the sum of all samples present in the feature table.                [optional]" name="psampleid" optional="False" type="text" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
    
  </outputs>

  <help><![CDATA[
Evaluate expected vs. observed taxonomic assignments
###############################################################

This visualizer compares a pair of observed and expected taxonomic
assignments to calculate precision, recall, and F-measure at each taxonomic
level, up to maximum level specified by the depth parameter. These metrics
are calculated at each semicolon-delimited rank. This action is useful for
comparing the accuracy of taxonomic assignment, e.g., between different
taxonomy classifiers or other bioinformatics methods. Expected taxonomies
should be derived from simulated or mock community sequences that have
known taxonomic affiliations.

Parameters
----------
expected_taxa : FeatureData[Taxonomy]
    Expected taxonomic assignments
observed_taxa : FeatureData[Taxonomy]
    Observed taxonomic assignments
depth : Int
    Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
    root, 7 = species for the greengenes reference sequence database).
palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
    Color palette to utilize for plotting.
require_exp_ids : Bool, optional
    Require that all features found in observed taxa must be found in
    expected taxa or raise error.
require_obs_ids : Bool, optional
    Require that all features found in expected taxa must be found in
    observed taxa or raise error.
feature_table : FeatureTable[RelativeFrequency], optional
    Optional feature table containing relative frequency of each feature,
    used to weight accuracy scores by frequency. Must contain all features
    found in expected and/or observed taxa. Features found in the table but
    not the expected/observed taxa will be dropped prior to analysis.
sample_id : Str, optional
    Optional sample ID to use for extracting frequency data from feature
    table, and for labeling accuracy results. If no sample_id is provided,
    feature frequencies are derived from the sum of all samples present in
    the feature table.

Returns
-------
visualization : Visualization
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>