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view qiime2/qiime_gneiss_dendrogram-heatmap.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 370e0b6e9826
children f190567fe3f6
line wrap: on
line source

<?xml version="1.0" ?>
<tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2019.4">
	<description> - Dendrogram heatmap.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime gneiss dendrogram-heatmap

--i-table=$itable
--i-tree=$itree
--m-metadata-column="$mmetadatacolumn"


#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 str($ppseudocount):
 --p-pseudocount=$ppseudocount
#end if

#if str($pndim):
 --p-ndim=$pndim
#end if

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

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

--o-visualization=ovisualization
;
qiime tools export --input-path 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"/>
		<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>

		<repeat name="input_files_mmetadatafile" optional="True" 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. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

	</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[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>