view qiime2/qiime_diversity_alpha-rarefaction.xml @ 15:276ec629f09a draft

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<?xml version="1.0" ?>
<tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction"
      version="2020.8">
  <description>Alpha rarefaction curves</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity alpha-rarefaction

--i-table=$itable

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

--p-max-depth=$pmaxdepth

#if str($pmetrics) != 'None':
--p-metrics=$pmetrics
#end if
# 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-min-depth=$pmindepth

--p-steps=$psteps

--p-iterations=$piterations

--o-visualization=ovisualization

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

;
cp oalphadiversity.qza $oalphadiversity

;
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 to compute rarefaction curves from. [required]" name="itable" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Optional phylogeny for phylogenetic metrics. Phylogeny[Rooted]                                               [optional]" name="iphylogeny" optional="False" type="data" />
    <param label="--p-max-depth: INTEGER   The maximum rarefaction depth. Must be greater than Range(1, None)        min-depth.                                [required]" name="pmaxdepth" optional="False" type="text" />
    <param label="--p-metrics: " multiple="True" name="pmetrics" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="observed_features">observed_features</option>
      <option value="heip_e">heip_e</option>
      <option value="dominance">dominance</option>
      <option value="goods_coverage">goods_coverage</option>
      <option value="ace">ace</option>
      <option value="gini_index">gini_index</option>
      <option value="simpson_e">simpson_e</option>
      <option value="pielou_e">pielou_e</option>
      <option value="mcintosh_e">mcintosh_e</option>
      <option value="berger_parker_d">berger_parker_d</option>
      <option value="shannon">shannon</option>
      <option value="enspie">enspie</option>
      <option value="mcintosh_d">mcintosh_d</option>
      <option value="lladser_pe">lladser_pe</option>
      <option value="brillouin_d">brillouin_d</option>
      <option value="menhinick">menhinick</option>
      <option value="simpson">simpson</option>
      <option value="margalef">margalef</option>
      <option value="robbins">robbins</option>
      <option value="doubles">doubles</option>
      <option value="chao1">chao1</option>
      <option value="michaelis_menten_fit">michaelis_menten_fit</option>
      <option value="singles">singles</option>
      <option value="faith_pd">faith_pd</option>
      <option value="fisher_alpha">fisher_alpha</option>
    </param>
    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments   The sample metadata. will be merged)                                                [optional]" name="additional_input" optional="True" type="data" />
    </repeat>
    <param label="--p-min-depth: INTEGER   The minimum rarefaction depth. Range(1, None)                                                [default: 1]" min="1" name="pmindepth" optional="True" type="integer" value="1" />
    <param label="--p-steps: INTEGER       The number of rarefaction depths to include between Range(2, None)        min-depth and max-depth.               [default: 10]" min="2" name="psteps" optional="True" type="integer" value="10" />
    <param label="--p-iterations: INTEGER  The number of rarefied feature tables to compute at Range(1, None)        each step.                             [default: 10]" min="1" name="piterations" optional="True" type="integer" value="10" />
    <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[
Alpha rarefaction curves
###############################################################

Generate interactive alpha rarefaction curves by computing rarefactions
between `min_depth` and `max_depth`. The number of intermediate depths to
compute is controlled by the `steps` parameter, with n `iterations` being
computed at each rarefaction depth. If sample metadata is provided, samples
may be grouped based on distinct values within a metadata column.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table to compute rarefaction curves from.
max_depth : Int % Range(1, None)
    The maximum rarefaction depth. Must be greater than min_depth.
phylogeny : Phylogeny[Rooted], optional
    Optional phylogeny for phylogenetic metrics.
metrics : Set[Str % Choices('mcintosh_e', 'chao1', 'observed_features', 'ace', 'margalef', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'heip_e', 'michaelis_menten_fit', 'enspie', 'faith_pd', 'menhinick', 'pielou_e', 'shannon', 'singles', 'simpson', 'fisher_alpha', 'dominance', 'robbins', 'lladser_pe', 'mcintosh_d', 'brillouin_d', 'goods_coverage')], optional
    The metrics to be measured. By default computes observed_features,
    shannon, and if phylogeny is provided, faith_pd.
metadata : Metadata, optional
    The sample metadata.
min_depth : Int % Range(1, None), optional
    The minimum rarefaction depth.
steps : Int % Range(2, None), optional
    The number of rarefaction depths to include between min_depth and
    max_depth.
iterations : Int % Range(1, None), optional
    The number of rarefied feature tables to compute at each step.

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