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view qiime_gneiss_dendrogram-heatmap.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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<?xml version="1.0" ?>
<tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2018.4">
	<description> - Dendrogram heatmap.</description>
	<requirements>
		<requirement type="package" version="2018.4">qiime2</requirement>
	</requirements>
	<command>
		<![CDATA[
	qiime gneiss dendrogram-heatmap --i-table=$itable
	#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 + ',' + d['additional_input'].__getattr__('file_name')
		#end for
		#return $file_list
	#end def
	 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn" --i-tree=$itree
	#if str($cmdconfig) != 'None':
	 --cmd-config=$cmdconfig
	#end if

	#if $pndim:
	 --p-ndim=$pndim
	#end if

	#if str($pcolormap) != 'None':
	 --p-color-map=$pcolormap
	#end if
	 --o-visualization=ovisualization
	#if str($pmethod) != 'None':
	 --p-method=$pmethod
	#end if
	;
	qiime tools export ovisualization.qzv --output-dir 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: FeatureTable[Composition] 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: 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.  [required]" name="itree" optional="False" type="data"/>

		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>
		<param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. Categorical metadata column to group the samples.  [required]" name="mmetadatacolumn" optional="False" type="text"/>

		<param label="--p-ndim: Number of dimensions to highlight. [default: 10]" name="pndim" optional="True" type="integer" value="10"/>

		<param label="--p-method: Specifies how the data should be normalized
                                  for display.Options include 'log' or 'clr'
                                  (default='clr').  [default: clr]" name="pmethod" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="log">log</option>
			<option value="clr">clr</option>
		</param>

		<param label="--p-color-map: Specifies the color map for plotting the
                                  heatmap. See https://matplotlib.org/examples
                                  /color/colormaps_reference.html for more
                                  details.  [default: viridis]" name="pcolormap" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="gist_heat">gist_heat</option>
			<option value="plasma">plasma</option>
			<option value="PiYG">PiYG</option>
			<option value="Pastel2">Pastel2</option>
			<option value="nipy_spectral">nipy_spectral</option>
			<option value="inferno">inferno</option>
			<option value="YlGn">YlGn</option>
			<option value="bone">bone</option>
			<option value="YlGnBu">YlGnBu</option>
			<option value="hsv">hsv</option>
			<option value="summer">summer</option>
			<option value="Set1">Set1</option>
			<option value="BrBG">BrBG</option>
			<option value="magma">magma</option>
			<option value="Paired">Paired</option>
			<option value="Vega10">Vega10</option>
			<option value="brg">brg</option>
			<option value="PuBu">PuBu</option>
			<option value="Spectral">Spectral</option>
			<option value="YlOrBr">YlOrBr</option>
			<option value="GnBu">GnBu</option>
			<option value="PuOr">PuOr</option>
			<option value="ocean">ocean</option>
			<option value="Reds">Reds</option>
			<option value="prism">prism</option>
			<option value="Vega20">Vega20</option>
			<option value="PuRd">PuRd</option>
			<option value="seismic">seismic</option>
			<option value="Dark2">Dark2</option>
			<option value="RdBu">RdBu</option>
			<option value="Accent">Accent</option>
			<option value="Set2">Set2</option>
			<option value="terrain">terrain</option>
			<option value="coolwarm">coolwarm</option>
			<option value="gnuplot">gnuplot</option>
			<option value="CMRmap">CMRmap</option>
			<option value="gnuplot2">gnuplot2</option>
			<option value="gist_ncar">gist_ncar</option>
			<option value="flag">flag</option>
			<option value="OrRd">OrRd</option>
			<option value="RdYlGn">RdYlGn</option>
			<option value="rainbow">rainbow</option>
			<option value="gist_rainbow">gist_rainbow</option>
			<option value="RdGy">RdGy</option>
			<option value="Pastel1">Pastel1</option>
			<option value="gist_earth">gist_earth</option>
			<option value="Set3">Set3</option>
			<option value="BuPu">BuPu</option>
			<option value="PRGn">PRGn</option>
			<option value="pink">pink</option>
			<option value="Purples">Purples</option>
			<option value="PuBuGn">PuBuGn</option>
			<option value="Vega20c">Vega20c</option>
			<option value="winter">winter</option>
			<option value="bwr">bwr</option>
			<option value="Vega20b">Vega20b</option>
			<option value="hot">hot</option>
			<option value="afmhot">afmhot</option>
			<option value="viridis">viridis</option>
			<option value="RdPu">RdPu</option>
			<option value="spring">spring</option>
			<option value="RdYlBu">RdYlBu</option>
			<option value="Greens">Greens</option>
			<option value="autumn">autumn</option>
			<option value="cubehelix">cubehelix</option>
			<option value="cool">cool</option>
			<option value="Blues">Blues</option>
			<option value="BuGn">BuGn</option>
			<option value="Greys">Greys</option>
			<option value="YlOrRd">YlOrRd</option>
			<option value="Oranges">Oranges</option>
			<option value="gray">gray</option>
			<option value="jet">jet</option>
			<option value="gist_stern">gist_stern</option>
			<option value="copper">copper</option>
		</param>

		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help><![CDATA[
Dendrogram heatmap.
--------------------

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[Composition]
    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.
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({'Accent', 'Blues', 'BrBG', 'BuGn', 'BuPu', 'CMRmap', 'Dark2', 'GnBu', 'Greens', 'Greys', 'OrRd', 'Oranges', 'PRGn', 'Paired', 'Pastel1', 'Pastel2', 'PiYG', 'PuBu', 'PuBuGn', 'PuOr', 'PuRd', 'Purples', 'RdBu', 'RdGy', 'RdPu', 'RdYlBu', 'RdYlGn', 'Reds', 'Set1', 'Set2', 'Set3', 'Spectral', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'brg', 'bwr', 'cool', 'coolwarm', 'copper', 'cubehelix', 'flag', 'gist_earth', 'gist_heat', 'gist_ncar', 'gist_rainbow', 'gist_stern', 'gnuplot', 'gnuplot2', 'gray', 'hot', 'hsv', 'inferno', 'jet', 'magma', 'nipy_spectral', 'ocean', 'pink', 'plasma', 'prism', 'rainbow', 'seismic', 'spring', 'summer', 'terrain', 'viridis', 'winter'}), 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>
</tool>