annotate qiime2/qiime_diversity_beta-rarefaction.xml @ 29:3ba9833030c1 draft

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<?xml version="1.0" ?>
<tool id="qiime_diversity_beta-rarefaction" name="qiime diversity beta-rarefaction"
      version="2020.8">
  <description>Beta diversity rarefaction</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity beta-rarefaction

--i-table=$itable

#if str($iphylogeny) != 'None':
--i-phylogeny=$iphylogeny
#end if

--p-metric=$pmetric

--p-clustering-method=$pclusteringmethod
# if $input_files_mmetadatafile:
  # def list_dict_to_string(list_dict):
    # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
    # for d in list_dict[1:]:
      # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
# end if

--p-sampling-depth=$psamplingdepth

--p-iterations=$piterations

#if str($pcorrelationmethod) != 'None':
--p-correlation-method=$pcorrelationmethod
#end if

#if str($pcolorscheme) != 'None':
--p-color-scheme=$pcolorscheme
#end if

--o-visualization=ovisualization

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

;
cp odistancematrix.qza $odistancematrix

;
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-table: ARTIFACT FeatureTable[Frequency] Feature table upon which to perform beta diversity rarefaction analyses.                     [required]" name="itable" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required for phylogenetic metrics]                                  [optional]" name="iphylogeny" optional="False" type="data" />
    <param label="--p-metric: " name="pmetric" optional="False" type="select">
      <option value="braycurtis">braycurtis</option>
      <option value="euclidean">euclidean</option>
      <option value="cityblock">cityblock</option>
      <option value="cosine">cosine</option>
      <option value="minkowski">minkowski</option>
      <option value="matching">matching</option>
      <option value="correlation">correlation</option>
      <option value="russellrao">russellrao</option>
      <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
      <option value="sokalsneath">sokalsneath</option>
      <option value="seuclidean">seuclidean</option>
      <option value="canberra">canberra</option>
      <option value="sokalmichener">sokalmichener</option>
      <option value="kulsinski">kulsinski</option>
      <option value="jensenshannon">jensenshannon</option>
      <option value="weighted_unifrac">weighted_unifrac</option>
      <option value="jaccard">jaccard</option>
      <option value="hamming">hamming</option>
      <option value="chebyshev">chebyshev</option>
      <option value="generalized_unifrac">generalized_unifrac</option>
      <option value="yule">yule</option>
      <option value="dice">dice</option>
      <option value="sqeuclidean">sqeuclidean</option>
      <option value="aitchison">aitchison</option>
      <option value="canberra_adkins">canberra_adkins</option>
      <option value="unweighted_unifrac">unweighted_unifrac</option>
      <option value="rogerstanimoto">rogerstanimoto</option>
    </param>
    <param label="--p-clustering-method: " name="pclusteringmethod" optional="False" type="select">
      <option value="upgma">upgma</option>
      <option value="nj">nj</option>
    </param>
    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments   The sample metadata used for the Emperor jackknifed will be merged)      PCoA plot.                                [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param label="--p-sampling-depth: INTEGER Range(1, None)        The total frequency that each sample should be rarefied to prior to computing the diversity metric. [required]" name="psamplingdepth" optional="False" type="text" />
    <param label="--p-iterations: INTEGER  Number of times to rarefy the feature table at a Range(2, None)        given sampling depth.                  [default: 10]" min="2" name="piterations" optional="True" type="integer" value="10" />
    <param label="--p-correlation-method: " name="pcorrelationmethod" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="pearson">pearson</option>
      <option value="spearman">spearman</option>
    </param>
    <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="BrBG">BrBG</option>
      <option value="BrBG_r">BrBG_r</option>
      <option value="PRGn">PRGn</option>
      <option value="PRGn_r">PRGn_r</option>
      <option value="PiYG">PiYG</option>
      <option value="PiYG_r">PiYG_r</option>
      <option value="PuOr">PuOr</option>
      <option value="PuOr_r">PuOr_r</option>
      <option value="RdBu">RdBu</option>
      <option value="RdBu_r">RdBu_r</option>
      <option value="RdGy">RdGy</option>
      <option value="RdGy_r">RdGy_r</option>
      <option value="RdYlBu">RdYlBu</option>
      <option value="RdYlBu_r">RdYlBu_r</option>
      <option value="RdYlGn">RdYlGn</option>
      <option value="RdYlGn_r">RdYlGn_r</option>
    </param>
    <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[
Beta diversity rarefaction
###############################################################

Repeatedly rarefy a feature table to compare beta diversity results within
a given rarefaction depth.  For a given beta diversity metric, this
visualizer will provide: an Emperor jackknifed PCoA plot, samples clustered
by UPGMA or neighbor joining with support calculation, and a heatmap
showing the correlation between rarefaction trials of that beta diversity
metric.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table upon which to perform beta diversity rarefaction
    analyses.
metric : Str % Choices('yule', 'weighted_normalized_unifrac', 'cityblock', 'weighted_unifrac', 'matching', 'russellrao', 'seuclidean', 'jaccard', 'braycurtis', 'minkowski', 'sokalmichener', 'aitchison', 'generalized_unifrac', 'canberra_adkins', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'sokalsneath', 'correlation', 'hamming', 'dice', 'rogerstanimoto', 'canberra', 'unweighted_unifrac', 'chebyshev', 'jensenshannon')
    The beta diversity metric to be computed.
clustering_method : Str % Choices('upgma', 'nj')
    Samples can be clustered with neighbor joining or UPGMA. An arbitrary
    rarefaction trial will be used for the tree, and the remaining trials
    are used to calculate the support of the internal nodes of that tree.
metadata : Metadata
    The sample metadata used for the Emperor jackknifed PCoA plot.
sampling_depth : Int % Range(1, None)
    The total frequency that each sample should be rarefied to prior to
    computing the diversity metric.
iterations : Int % Range(2, None), optional
    Number of times to rarefy the feature table at a given sampling depth.
phylogeny : Phylogeny[Rooted], optional
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree. [required for phylogenetic metrics]
correlation_method : Str % Choices('spearman', 'pearson'), optional
    The Mantel correlation test to be applied when computing correlation
    between beta diversity distance matrices.
color_scheme : Str % Choices('BrBG', 'BrBG_r', 'PRGn', 'PRGn_r', 'PiYG', 'PiYG_r', 'PuOr', 'PuOr_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r'), optional
    The matplotlib color scheme to generate the heatmap with.

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