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comparison qiime2/qiime_gneiss_dendrogram-heatmap.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2018.4">
3 <description> - Dendrogram heatmap.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime gneiss dendrogram-heatmap --i-table=$itable
10 #def list_dict_to_string(list_dict):
11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
12 #for d in list_dict[1:]:
13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
14 #end for
15 #return $file_list
16 #end def
17 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn" --i-tree=$itree
18 #if str($cmdconfig) != 'None':
19 --cmd-config=$cmdconfig
20 #end if
21
22 #if $pndim:
23 --p-ndim=$pndim
24 #end if
25
26 #if str($pcolormap) != 'None':
27 --p-color-map=$pcolormap
28 #end if
29 --o-visualization=ovisualization
30 #if str($pmethod) != 'None':
31 --p-method=$pmethod
32 #end if
33 ;
34 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
35 && cp -r out/* '$ovisualization.files_path'
36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
37 ]]>
38 </command>
39 <inputs>
40 <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"/>
41 <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"/>
42
43 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
44 <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" />
45 </repeat>
46 <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"/>
47
48 <param label="--p-ndim: Number of dimensions to highlight. [default: 10]" name="pndim" optional="True" type="integer" value="10"/>
49
50 <param label="--p-method: Specifies how the data should be normalized
51 for display.Options include 'log' or 'clr'
52 (default='clr'). [default: clr]" name="pmethod" optional="True" type="select">
53 <option selected="True" value="None">Selection is Optional</option>
54 <option value="log">log</option>
55 <option value="clr">clr</option>
56 </param>
57
58 <param label="--p-color-map: Specifies the color map for plotting the
59 heatmap. See https://matplotlib.org/examples
60 /color/colormaps_reference.html for more
61 details. [default: viridis]" name="pcolormap" optional="True" type="select">
62 <option selected="True" value="None">Selection is Optional</option>
63 <option value="gist_heat">gist_heat</option>
64 <option value="plasma">plasma</option>
65 <option value="PiYG">PiYG</option>
66 <option value="Pastel2">Pastel2</option>
67 <option value="nipy_spectral">nipy_spectral</option>
68 <option value="inferno">inferno</option>
69 <option value="YlGn">YlGn</option>
70 <option value="bone">bone</option>
71 <option value="YlGnBu">YlGnBu</option>
72 <option value="hsv">hsv</option>
73 <option value="summer">summer</option>
74 <option value="Set1">Set1</option>
75 <option value="BrBG">BrBG</option>
76 <option value="magma">magma</option>
77 <option value="Paired">Paired</option>
78 <option value="Vega10">Vega10</option>
79 <option value="brg">brg</option>
80 <option value="PuBu">PuBu</option>
81 <option value="Spectral">Spectral</option>
82 <option value="YlOrBr">YlOrBr</option>
83 <option value="GnBu">GnBu</option>
84 <option value="PuOr">PuOr</option>
85 <option value="ocean">ocean</option>
86 <option value="Reds">Reds</option>
87 <option value="prism">prism</option>
88 <option value="Vega20">Vega20</option>
89 <option value="PuRd">PuRd</option>
90 <option value="seismic">seismic</option>
91 <option value="Dark2">Dark2</option>
92 <option value="RdBu">RdBu</option>
93 <option value="Accent">Accent</option>
94 <option value="Set2">Set2</option>
95 <option value="terrain">terrain</option>
96 <option value="coolwarm">coolwarm</option>
97 <option value="gnuplot">gnuplot</option>
98 <option value="CMRmap">CMRmap</option>
99 <option value="gnuplot2">gnuplot2</option>
100 <option value="gist_ncar">gist_ncar</option>
101 <option value="flag">flag</option>
102 <option value="OrRd">OrRd</option>
103 <option value="RdYlGn">RdYlGn</option>
104 <option value="rainbow">rainbow</option>
105 <option value="gist_rainbow">gist_rainbow</option>
106 <option value="RdGy">RdGy</option>
107 <option value="Pastel1">Pastel1</option>
108 <option value="gist_earth">gist_earth</option>
109 <option value="Set3">Set3</option>
110 <option value="BuPu">BuPu</option>
111 <option value="PRGn">PRGn</option>
112 <option value="pink">pink</option>
113 <option value="Purples">Purples</option>
114 <option value="PuBuGn">PuBuGn</option>
115 <option value="Vega20c">Vega20c</option>
116 <option value="winter">winter</option>
117 <option value="bwr">bwr</option>
118 <option value="Vega20b">Vega20b</option>
119 <option value="hot">hot</option>
120 <option value="afmhot">afmhot</option>
121 <option value="viridis">viridis</option>
122 <option value="RdPu">RdPu</option>
123 <option value="spring">spring</option>
124 <option value="RdYlBu">RdYlBu</option>
125 <option value="Greens">Greens</option>
126 <option value="autumn">autumn</option>
127 <option value="cubehelix">cubehelix</option>
128 <option value="cool">cool</option>
129 <option value="Blues">Blues</option>
130 <option value="BuGn">BuGn</option>
131 <option value="Greys">Greys</option>
132 <option value="YlOrRd">YlOrRd</option>
133 <option value="Oranges">Oranges</option>
134 <option value="gray">gray</option>
135 <option value="jet">jet</option>
136 <option value="gist_stern">gist_stern</option>
137 <option value="copper">copper</option>
138 </param>
139
140 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
141 </inputs>
142 <outputs>
143 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
144 </outputs>
145 <help><![CDATA[
146 Dendrogram heatmap.
147 --------------------
148
149 Visualize the feature table as a heatmap, with samples sorted along a
150 specified categorical metadata column and features clustered together
151 specified by the tree.
152
153 Parameters
154 ----------
155 table : FeatureTable[Composition]
156 The feature table that will be plotted as a heatmap. This table is
157 assumed to have strictly positive values.
158 tree : Hierarchy
159 A hierarchy of feature identifiers where each tipcorresponds to the
160 feature identifiers in the table. This tree can contain tip ids that
161 are not present in the table, but all feature ids in the table must be
162 present in this tree.
163 metadata : MetadataColumn[Categorical]
164 Categorical metadata column to group the samples.
165 ndim : Int, optional
166 Number of dimensions to highlight.
167 method : Str % Choices({'clr', 'log'}), optional
168 Specifies how the data should be normalized for display.Options include
169 'log' or 'clr' (default='clr').
170 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
171 Specifies the color map for plotting the heatmap. See
172 https://matplotlib.org/examples/color/colormaps_reference.html for more
173 details.
174
175 Returns
176 -------
177 visualization : Visualization
178 \
179 ]]>
180 </help>
181 <macros>
182 <import>qiime_citation.xml</import>
183 </macros>
184 <expand macro="qiime_citation" />
185 </tool>