diff qiime2/qiime_gneiss_dendrogram-heatmap.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_dendrogram-heatmap.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,187 @@
+<?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 $ppseudocount:
+ --p-pseudocount=$ppseudocount
+#end if
+
+#if $pndim:
+ --p-ndim=$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>