annotate qiime2/qiime_gneiss_dendrogram-heatmap.xml @ 29:3ba9833030c1 draft

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<?xml version="1.0" ?>
<tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap"
      version="2020.8">
  <description>Dendrogram heatmap.</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime gneiss dendrogram-heatmap

--i-table=$itable

--i-tree=$itree
# 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

#if '__ob__' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if
#if '__cb__' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if
#if 'X' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if
#if '__sq__' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if
#if '__db__' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if

--m-metadata-column=$mmetadatacolumn


--p-pseudocount=$ppseudocount

--p-ndim=$pndim

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

#if str($pcolormap) != 'None':
--p-color-map=$pcolormap
#end if

--o-visualization=ovisualization

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

;
cp oclustering.qza $oclustering

;
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] The feature table that will be plotted as a heatmap. This table is assumed to have strictly positive values.                          [required]" name="itable" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT       A hierarchy of feature identifiers where each Hierarchy             tipcorresponds 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]" name="itree" optional="False" type="data" />
    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
    </repeat>
    <param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] Categorical metadata column to group the samples. [required]" name="mmetadatacolumn" optional="False" type="text" />
    <param label="--p-pseudocount: NUMBER  The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" />
    <param label="--p-ndim: INTEGER        Number of dimensions to highlight.     [default: 10]" name="pndim" optional="True" type="integer" value="10" />
    <param label="--p-method: " name="pmethod" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="clr">clr</option>
      <option value="log">log</option>
    </param>
    <param label="--p-color-map: " name="pcolormap" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="viridis">viridis</option>
      <option value="inferno">inferno</option>
      <option value="plasma">plasma</option>
      <option value="magma">magma</option>
      <option value="Blues">Blues</option>
      <option value="BuGn">BuGn</option>
      <option value="BuPu">BuPu</option>
      <option value="GnBu">GnBu</option>
      <option value="Greens">Greens</option>
      <option value="Greys">Greys</option>
      <option value="Oranges">Oranges</option>
      <option value="OrRd">OrRd</option>
      <option value="PuBu">PuBu</option>
      <option value="PuBuGn">PuBuGn</option>
      <option value="PuRd">PuRd</option>
      <option value="Purples">Purples</option>
      <option value="RdPu">RdPu</option>
      <option value="Reds">Reds</option>
      <option value="YlGn">YlGn</option>
      <option value="YlGnBu">YlGnBu</option>
      <option value="YlOrBr">YlOrBr</option>
      <option value="YlOrRd">YlOrRd</option>
      <option value="afmhot">afmhot</option>
      <option value="autumn">autumn</option>
      <option value="bone">bone</option>
      <option value="cool">cool</option>
      <option value="copper">copper</option>
      <option value="gist_heat">gist_heat</option>
      <option value="gray">gray</option>
      <option value="hot">hot</option>
      <option value="pink">pink</option>
      <option value="spring">spring</option>
      <option value="summer">summer</option>
      <option value="winter">winter</option>
      <option value="BrBG">BrBG</option>
      <option value="bwr">bwr</option>
      <option value="coolwarm">coolwarm</option>
      <option value="PiYG">PiYG</option>
      <option value="PRGn">PRGn</option>
      <option value="PuOr">PuOr</option>
      <option value="RdBu">RdBu</option>
      <option value="RdGy">RdGy</option>
      <option value="RdYlBu">RdYlBu</option>
      <option value="RdYlGn">RdYlGn</option>
      <option value="Spectral">Spectral</option>
      <option value="seismic">seismic</option>
      <option value="Accent">Accent</option>
      <option value="Dark2">Dark2</option>
      <option value="Paired">Paired</option>
      <option value="Pastel1">Pastel1</option>
      <option value="Pastel2">Pastel2</option>
      <option value="Set1">Set1</option>
      <option value="Set2">Set2</option>
      <option value="Set3">Set3</option>
      <option value="Vega10">Vega10</option>
      <option value="Vega20">Vega20</option>
      <option value="Vega20b">Vega20b</option>
      <option value="Vega20c">Vega20c</option>
      <option value="gist_earth">gist_earth</option>
      <option value="terrain">terrain</option>
      <option value="ocean">ocean</option>
      <option value="gist_stern">gist_stern</option>
      <option value="brg">brg</option>
      <option value="CMRmap">CMRmap</option>
      <option value="cubehelix">cubehelix</option>
      <option value="gnuplot">gnuplot</option>
      <option value="gnuplot2">gnuplot2</option>
      <option value="gist_ncar">gist_ncar</option>
      <option value="nipy_spectral">nipy_spectral</option>
      <option value="jet">jet</option>
      <option value="rainbow">rainbow</option>
      <option value="gist_rainbow">gist_rainbow</option>
      <option value="hsv">hsv</option>
      <option value="flag">flag</option>
      <option value="prism">prism</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[
Dendrogram heatmap.
###############################################################

.. deprecated::
   This Visualizer is deprecated and will be removed in a future version of
   this plugin.

Visualize the feature table as a heatmap, with samples sorted along a
specified categorical metadata column and features clustered together
specified by the tree.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table that will be plotted as a heatmap. This table is
    assumed to have strictly positive values.
tree : Hierarchy
    A hierarchy of feature identifiers where each tipcorresponds 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.
metadata : MetadataColumn[Categorical]
    Categorical metadata column to group the samples.
pseudocount : Float, optional
    The pseudocount to add to avoid division by zero.
ndim : Int, optional
    Number of dimensions to highlight.
method : Str % Choices('clr', 'log'), optional
    Specifies how the data should be normalized for display.Options include
    'log' or 'clr' (default='clr').
color_map : Str % Choices('viridis', 'inferno', 'plasma', 'magma', 'Blues', 'BuGn', 'BuPu', 'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd', 'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu', 'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'cool', 'copper', 'gist_heat', 'gray', 'hot', 'pink', 'spring', 'summer', 'winter', 'BrBG', 'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral', 'seismic', 'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'gist_earth', 'terrain', 'ocean', 'gist_stern', 'brg', 'CMRmap', 'cubehelix', 'gnuplot', 'gnuplot2', 'gist_ncar', 'nipy_spectral', 'jet', 'rainbow', 'gist_rainbow', 'hsv', 'flag', 'prism'), optional
    Specifies the color map for plotting the heatmap. See
    https://matplotlib.org/examples/color/colormaps_reference.html for more
    details.

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