view qiime2/qiime_feature-table_heatmap.xml @ 14:a0a8d77a991c draft

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<?xml version="1.0" ?>
<tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap"
      version="2020.8">
  <description>Generate a heatmap representation of a feature table</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime feature-table heatmap

--i-table=$itable
# if $input_files_msamplemetadatafile:
  # 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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
# end if

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

#if str($msamplemetadatacolumn):
  --m-sample-metadata-column=$msamplemetadatacolumn
#end if
# if $input_files_mfeaturemetadatafile:
  # 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-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
# end if

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

#if str($mfeaturemetadatacolumn):
  --m-feature-metadata-column=$mfeaturemetadatacolumn
#end if

#if $pnonormalize:
 --p-no-normalize
#end if

#if str($ptitle):
  --p-title=$ptitle
#end if
#if str($pmetric) != 'None':
--p-metric=$pmetric
#end if

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

#if str($pcluster) != 'None':
--p-cluster=$pcluster
#end if

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

--o-visualization=ovisualization

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

;
cp ogroupedtable.qza $ogroupedtable

;
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 to visualize.            [required]" name="itable" optional="False" type="data" />
    <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
    </repeat>
    <param label="--m-sample-metadata-column: COLUMN  MetadataColumn[Categorical] Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`=\'feature\', samples will be sorted by the metadata values.                           [optional]" name="msamplemetadatacolumn" optional="False" type="text" />
    <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
    </repeat>
    <param label="--m-feature-metadata-column: COLUMN  MetadataColumn[Categorical] Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`=\'sample\', features will be sorted by the metadata values.                           [optional]" name="mfeaturemetadatacolumn" optional="False" type="text" />
    <param label="--p-no-normalize: Do not normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table. [default: True]" name="pnonormalize" selected="False" type="boolean" />
    <param label="--p-title: TEXT         Optional custom plot title.                [optional]" name="ptitle" optional="False" type="text" />
    <param label="--p-metric: " name="pmetric" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="euclidean">euclidean</option>
      <option value="cityblock">cityblock</option>
      <option value="matching">matching</option>
      <option value="russellrao">russellrao</option>
      <option value="sokalmichener">sokalmichener</option>
      <option value="kulsinski">kulsinski</option>
      <option value="chebyshev">chebyshev</option>
      <option value="hamming">hamming</option>
      <option value="dice">dice</option>
      <option value="yule">yule</option>
      <option value="rogerstanimoto">rogerstanimoto</option>
      <option value="braycurtis">braycurtis</option>
      <option value="cosine">cosine</option>
      <option value="minkowski">minkowski</option>
      <option value="correlation">correlation</option>
      <option value="sokalsneath">sokalsneath</option>
      <option value="seuclidean">seuclidean</option>
      <option value="canberra">canberra</option>
      <option value="mahalanobis">mahalanobis</option>
      <option value="jaccard">jaccard</option>
      <option value="sqeuclidean">sqeuclidean</option>
    </param>
    <param label="--p-method: " name="pmethod" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="centroid">centroid</option>
      <option value="median">median</option>
      <option value="weighted">weighted</option>
      <option value="average">average</option>
      <option value="single">single</option>
      <option value="complete">complete</option>
      <option value="ward">ward</option>
    </param>
    <param label="--p-cluster: " name="pcluster" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="both">both</option>
      <option value="none">none</option>
      <option value="features">features</option>
      <option value="samples">samples</option>
    </param>
    <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Spectral">Spectral</option>
      <option value="flag">flag</option>
      <option value="jet">jet</option>
      <option value="Vega20">Vega20</option>
      <option value="terrain">terrain</option>
      <option value="jet_r">jet_r</option>
      <option value="Vega20c_r">Vega20c_r</option>
      <option value="Oranges_r">Oranges_r</option>
      <option value="spectral">spectral</option>
      <option value="summer">summer</option>
      <option value="BuPu_r">BuPu_r</option>
      <option value="tab20b_r">tab20b_r</option>
      <option value="Pastel1">Pastel1</option>
      <option value="gnuplot_r">gnuplot_r</option>
      <option value="seismic">seismic</option>
      <option value="icefire">icefire</option>
      <option value="Set1">Set1</option>
      <option value="bwr">bwr</option>
      <option value="coolwarm_r">coolwarm_r</option>
      <option value="ocean_r">ocean_r</option>
      <option value="gist_gray_r">gist_gray_r</option>
      <option value="autumn">autumn</option>
      <option value="BrBG">BrBG</option>
      <option value="Pastel2">Pastel2</option>
      <option value="GnBu">GnBu</option>
      <option value="Vega20b_r">Vega20b_r</option>
      <option value="tab20c">tab20c</option>
      <option value="Paired">Paired</option>
      <option value="YlOrRd_r">YlOrRd_r</option>
      <option value="icefire_r">icefire_r</option>
      <option value="cubehelix_r">cubehelix_r</option>
      <option value="CMRmap_r">CMRmap_r</option>
      <option value="RdBu">RdBu</option>
      <option value="YlGn_r">YlGn_r</option>
      <option value="gray_r">gray_r</option>
      <option value="mako_r">mako_r</option>
      <option value="OrRd_r">OrRd_r</option>
      <option value="Vega10">Vega10</option>
      <option value="Set3">Set3</option>
      <option value="RdYlGn_r">RdYlGn_r</option>
      <option value="hsv">hsv</option>
      <option value="cool_r">cool_r</option>
      <option value="Spectral_r">Spectral_r</option>
      <option value="rainbow">rainbow</option>
      <option value="cividis">cividis</option>
      <option value="Blues_r">Blues_r</option>
      <option value="PuOr_r">PuOr_r</option>
      <option value="binary_r">binary_r</option>
      <option value="RdGy">RdGy</option>
      <option value="Pastel2_r">Pastel2_r</option>
      <option value="Pastel1_r">Pastel1_r</option>
      <option value="Dark2">Dark2</option>
      <option value="vlag">vlag</option>
      <option value="binary">binary</option>
      <option value="pink">pink</option>
      <option value="Purples">Purples</option>
      <option value="cividis_r">cividis_r</option>
      <option value="gray">gray</option>
      <option value="seismic_r">seismic_r</option>
      <option value="Greys">Greys</option>
      <option value="tab20">tab20</option>
      <option value="BuPu">BuPu</option>
      <option value="RdBu_r">RdBu_r</option>
      <option value="gnuplot2_r">gnuplot2_r</option>
      <option value="Accent_r">Accent_r</option>
      <option value="magma">magma</option>
      <option value="copper_r">copper_r</option>
      <option value="inferno">inferno</option>
      <option value="nipy_spectral_r">nipy_spectral_r</option>
      <option value="pink_r">pink_r</option>
      <option value="copper">copper</option>
      <option value="Dark2_r">Dark2_r</option>
      <option value="YlGnBu_r">YlGnBu_r</option>
      <option value="Wistia_r">Wistia_r</option>
      <option value="spectral_r">spectral_r</option>
      <option value="cubehelix">cubehelix</option>
      <option value="tab20_r">tab20_r</option>
      <option value="viridis">viridis</option>
      <option value="RdYlBu">RdYlBu</option>
      <option value="Blues">Blues</option>
      <option value="rocket_r">rocket_r</option>
      <option value="Set1_r">Set1_r</option>
      <option value="brg_r">brg_r</option>
      <option value="bone_r">bone_r</option>
      <option value="gist_ncar_r">gist_ncar_r</option>
      <option value="afmhot">afmhot</option>
      <option value="RdYlBu_r">RdYlBu_r</option>
      <option value="gist_earth_r">gist_earth_r</option>
      <option value="RdGy_r">RdGy_r</option>
      <option value="Vega10_r">Vega10_r</option>
      <option value="gist_rainbow_r">gist_rainbow_r</option>
      <option value="spring">spring</option>
      <option value="Set3_r">Set3_r</option>
      <option value="magma_r">magma_r</option>
      <option value="mako">mako</option>
      <option value="PuRd">PuRd</option>
      <option value="gnuplot2">gnuplot2</option>
      <option value="Paired_r">Paired_r</option>
      <option value="Vega20b">Vega20b</option>
      <option value="Accent">Accent</option>
      <option value="hsv_r">hsv_r</option>
      <option value="ocean">ocean</option>
      <option value="gist_earth">gist_earth</option>
      <option value="afmhot_r">afmhot_r</option>
      <option value="bone">bone</option>
      <option value="rocket">rocket</option>
      <option value="RdYlGn">RdYlGn</option>
      <option value="bwr_r">bwr_r</option>
      <option value="RdPu_r">RdPu_r</option>
      <option value="BuGn">BuGn</option>
      <option value="PuBu">PuBu</option>
      <option value="hot_r">hot_r</option>
      <option value="Vega20c">Vega20c</option>
      <option value="gist_yarg">gist_yarg</option>
      <option value="tab10">tab10</option>
      <option value="coolwarm">coolwarm</option>
      <option value="winter_r">winter_r</option>
      <option value="plasma_r">plasma_r</option>
      <option value="Wistia">Wistia</option>
      <option value="BuGn_r">BuGn_r</option>
      <option value="Set2">Set2</option>
      <option value="Vega20_r">Vega20_r</option>
      <option value="hot">hot</option>
      <option value="brg">brg</option>
      <option value="BrBG_r">BrBG_r</option>
      <option value="gist_heat">gist_heat</option>
      <option value="YlOrRd">YlOrRd</option>
      <option value="inferno_r">inferno_r</option>
      <option value="viridis_r">viridis_r</option>
      <option value="gist_stern_r">gist_stern_r</option>
      <option value="tab20c_r">tab20c_r</option>
      <option value="gist_gray">gist_gray</option>
      <option value="Reds_r">Reds_r</option>
      <option value="flag_r">flag_r</option>
      <option value="Purples_r">Purples_r</option>
      <option value="vlag_r">vlag_r</option>
      <option value="summer_r">summer_r</option>
      <option value="Greys_r">Greys_r</option>
      <option value="PRGn">PRGn</option>
      <option value="PiYG">PiYG</option>
      <option value="gist_ncar">gist_ncar</option>
      <option value="Oranges">Oranges</option>
      <option value="Reds">Reds</option>
      <option value="GnBu_r">GnBu_r</option>
      <option value="RdPu">RdPu</option>
      <option value="YlOrBr_r">YlOrBr_r</option>
      <option value="autumn_r">autumn_r</option>
      <option value="YlGn">YlGn</option>
      <option value="CMRmap">CMRmap</option>
      <option value="gnuplot">gnuplot</option>
      <option value="rainbow_r">rainbow_r</option>
      <option value="PiYG_r">PiYG_r</option>
      <option value="Greens">Greens</option>
      <option value="YlOrBr">YlOrBr</option>
      <option value="prism_r">prism_r</option>
      <option value="winter">winter</option>
      <option value="gist_yarg_r">gist_yarg_r</option>
      <option value="Set2_r">Set2_r</option>
      <option value="nipy_spectral">nipy_spectral</option>
      <option value="plasma">plasma</option>
      <option value="OrRd">OrRd</option>
      <option value="Greens_r">Greens_r</option>
      <option value="tab10_r">tab10_r</option>
      <option value="YlGnBu">YlGnBu</option>
      <option value="prism">prism</option>
      <option value="PRGn_r">PRGn_r</option>
      <option value="gist_heat_r">gist_heat_r</option>
      <option value="terrain_r">terrain_r</option>
      <option value="tab20b">tab20b</option>
      <option value="PuBuGn">PuBuGn</option>
      <option value="PuBu_r">PuBu_r</option>
      <option value="spring_r">spring_r</option>
      <option value="gist_rainbow">gist_rainbow</option>
      <option value="cool">cool</option>
      <option value="PuOr">PuOr</option>
      <option value="PuRd_r">PuRd_r</option>
      <option value="gist_stern">gist_stern</option>
      <option value="PuBuGn_r">PuBuGn_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[
Generate a heatmap representation of a feature table
###############################################################

Generate a heatmap representation of a feature table with optional
clustering on both the sample and feature axes.  Tip: To generate a heatmap
containing taxonomic annotations, use `qiime taxa collapse` to collapse the
feature table at the desired taxonomic level.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table to visualize.
sample_metadata : MetadataColumn[Categorical], optional
    Annotate the sample IDs with these sample metadata values. When
    metadata is present and `cluster`='feature', samples will be sorted by
    the metadata values.
feature_metadata : MetadataColumn[Categorical], optional
    Annotate the feature IDs with these feature metadata values. When
    metadata is present and `cluster`='sample', features will be sorted by
    the metadata values.
normalize : Bool, optional
    Normalize the feature table by adding a psuedocount of 1 and then
    taking the log10 of the table.
title : Str, optional
    Optional custom plot title.
metric : Str % Choices('yule', 'seuclidean', 'sokalmichener', 'sokalsneath', 'hamming', 'canberra', 'cityblock', 'russellrao', 'jaccard', 'braycurtis', 'minkowski', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'correlation', 'dice', 'rogerstanimoto', 'mahalanobis', 'chebyshev', 'matching'), optional
    Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
    born.clustermap.html#seaborn.clustermap for more detail).
method : Str % Choices('complete', 'average', 'ward', 'median', 'weighted', 'centroid', 'single'), optional
    Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
    nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
cluster : Str % Choices('both', 'features', 'none', 'samples'), optional
    Specify which axes to cluster.
color_scheme : Str % Choices('YlGn', 'flag', 'Greens_r', 'RdPu_r', 'OrRd', 'Set1_r', 'RdYlGn', 'inferno_r', 'Accent_r', 'bwr', 'PuOr', 'seismic_r', 'RdGy_r', 'tab20b_r', 'Oranges', 'spectral', 'RdYlGn_r', 'nipy_spectral_r', 'gist_gray', 'binary', 'gist_yarg_r', 'cubehelix', 'viridis_r', 'autumn', 'bone_r', 'terrain_r', 'RdPu', 'inferno', 'PRGn', 'YlGnBu', 'mako', 'gray', 'tab20_r', 'Oranges_r', 'gist_stern_r', 'Dark2_r', 'Purples_r', 'coolwarm', 'RdYlBu', 'tab10', 'copper_r', 'YlOrRd_r', 'gray_r', 'magma', 'Set3_r', 'BuGn', 'viridis', 'icefire_r', 'PuOr_r', 'YlOrBr', 'winter_r', 'hsv', 'gist_earth_r', 'rocket_r', 'Vega20b', 'autumn_r', 'gnuplot', 'Paired', 'PuRd_r', 'BrBG_r', 'plasma_r', 'Set2', 'prism', 'winter', 'seismic', 'RdGy', 'Blues_r', 'Reds_r', 'gist_ncar_r', 'Reds', 'afmhot', 'Greys', 'rainbow', 'tab10_r', 'GnBu_r', 'gnuplot2', 'pink', 'tab20b', 'BuGn_r', 'PuRd', 'gist_stern', 'magma_r', 'prism_r', 'tab20c_r', 'BuPu', 'cividis_r', 'BrBG', 'Wistia_r', 'gist_gray_r', 'ocean_r', 'summer_r', 'mako_r', 'CMRmap_r', 'cool_r', 'coolwarm_r', 'Greens', 'RdBu', 'icefire', 'spectral_r', 'Vega20', 'brg', 'Paired_r', 'BuPu_r', 'gist_rainbow', 'CMRmap', 'cool', 'gist_earth', 'bwr_r', 'rocket', 'YlGn_r', 'Vega20b_r', 'Wistia', 'Vega20c_r', 'Accent', 'plasma', 'Set1', 'PuBu_r', 'Purples', 'RdYlBu_r', 'brg_r', 'flag_r', 'Set3', 'hot_r', 'Blues', 'Pastel1_r', 'YlOrBr_r', 'hsv_r', 'Pastel2', 'Pastel1', 'bone', 'tab20', 'PuBuGn_r', 'terrain', 'gist_rainbow_r', 'Spectral_r', 'Pastel2_r', 'RdBu_r', 'summer', 'gist_ncar', 'OrRd_r', 'copper', 'tab20c', 'PuBuGn', 'Set2_r', 'vlag', 'jet_r', 'gist_heat_r', 'PRGn_r', 'Vega10', 'jet', 'Spectral', 'rainbow_r', 'binary_r', 'ocean', 'spring', 'Dark2', 'Vega20_r', 'vlag_r', 'PiYG', 'PuBu', 'YlGnBu_r', 'afmhot_r', 'nipy_spectral', 'gnuplot2_r', 'cividis', 'gnuplot_r', 'Greys_r', 'cubehelix_r', 'spring_r', 'PiYG_r', 'gist_yarg', 'gist_heat', 'Vega20c', 'GnBu', 'YlOrRd', 'hot', 'Vega10_r', 'pink_r'), optional
    The matplotlib colorscheme to generate the heatmap with.

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