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comparison qiime2-2020.8/qiime_gneiss_dendrogram-heatmap.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap"
3 version="2020.8">
4 <description>Dendrogram heatmap.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime gneiss dendrogram-heatmap
10
11 --i-table=$itable
12
13 --i-tree=$itree
14 # if $input_files_mmetadatafile:
15 # def list_dict_to_string(list_dict):
16 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 # for d in list_dict[1:]:
18 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
19 # end for
20 # return $file_list
21 # end def
22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
23 # end if
24
25 #if '__ob__' in str($mmetadatacolumn):
26 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
27 #set $mmetadatacolumn = $mmetadatacolumn_temp
28 #end if
29 #if '__cb__' in str($mmetadatacolumn):
30 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
31 #set $mmetadatacolumn = $mmetadatacolumn_temp
32 #end if
33 #if 'X' in str($mmetadatacolumn):
34 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
35 #set $mmetadatacolumn = $mmetadatacolumn_temp
36 #end if
37 #if '__sq__' in str($mmetadatacolumn):
38 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
39 #set $mmetadatacolumn = $mmetadatacolumn_temp
40 #end if
41 #if '__db__' in str($mmetadatacolumn):
42 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
43 #set $mmetadatacolumn = $mmetadatacolumn_temp
44 #end if
45
46 --m-metadata-column=$mmetadatacolumn
47
48
49 --p-pseudocount=$ppseudocount
50
51 --p-ndim=$pndim
52
53 #if str($pmethod) != 'None':
54 --p-method=$pmethod
55 #end if
56
57 #if str($pcolormap) != 'None':
58 --p-color-map=$pcolormap
59 #end if
60
61 --o-visualization=ovisualization
62
63 #if str($examples) != 'None':
64 --examples=$examples
65 #end if
66
67 ;
68 cp oclustering.qza $oclustering
69
70 ;
71 qiime tools export ovisualization.qzv --output-path out
72 && mkdir -p '$ovisualization.files_path'
73 && cp -r out/* '$ovisualization.files_path'
74 && mv '$ovisualization.files_path/index.html' '$ovisualization'
75
76 ]]></command>
77 <inputs>
78 <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" />
79 <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" />
80 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
81 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
82 </repeat>
83 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to group the samples. [required]" name="mmetadatacolumn" optional="False" type="text" />
84 <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" />
85 <param label="--p-ndim: INTEGER Number of dimensions to highlight. [default: 10]" name="pndim" optional="True" type="integer" value="10" />
86 <param label="--p-method: " name="pmethod" optional="True" type="select">
87 <option selected="True" value="None">Selection is Optional</option>
88 <option value="clr">clr</option>
89 <option value="log">log</option>
90 </param>
91 <param label="--p-color-map: " name="pcolormap" optional="True" type="select">
92 <option selected="True" value="None">Selection is Optional</option>
93 <option value="viridis">viridis</option>
94 <option value="inferno">inferno</option>
95 <option value="plasma">plasma</option>
96 <option value="magma">magma</option>
97 <option value="Blues">Blues</option>
98 <option value="BuGn">BuGn</option>
99 <option value="BuPu">BuPu</option>
100 <option value="GnBu">GnBu</option>
101 <option value="Greens">Greens</option>
102 <option value="Greys">Greys</option>
103 <option value="Oranges">Oranges</option>
104 <option value="OrRd">OrRd</option>
105 <option value="PuBu">PuBu</option>
106 <option value="PuBuGn">PuBuGn</option>
107 <option value="PuRd">PuRd</option>
108 <option value="Purples">Purples</option>
109 <option value="RdPu">RdPu</option>
110 <option value="Reds">Reds</option>
111 <option value="YlGn">YlGn</option>
112 <option value="YlGnBu">YlGnBu</option>
113 <option value="YlOrBr">YlOrBr</option>
114 <option value="YlOrRd">YlOrRd</option>
115 <option value="afmhot">afmhot</option>
116 <option value="autumn">autumn</option>
117 <option value="bone">bone</option>
118 <option value="cool">cool</option>
119 <option value="copper">copper</option>
120 <option value="gist_heat">gist_heat</option>
121 <option value="gray">gray</option>
122 <option value="hot">hot</option>
123 <option value="pink">pink</option>
124 <option value="spring">spring</option>
125 <option value="summer">summer</option>
126 <option value="winter">winter</option>
127 <option value="BrBG">BrBG</option>
128 <option value="bwr">bwr</option>
129 <option value="coolwarm">coolwarm</option>
130 <option value="PiYG">PiYG</option>
131 <option value="PRGn">PRGn</option>
132 <option value="PuOr">PuOr</option>
133 <option value="RdBu">RdBu</option>
134 <option value="RdGy">RdGy</option>
135 <option value="RdYlBu">RdYlBu</option>
136 <option value="RdYlGn">RdYlGn</option>
137 <option value="Spectral">Spectral</option>
138 <option value="seismic">seismic</option>
139 <option value="Accent">Accent</option>
140 <option value="Dark2">Dark2</option>
141 <option value="Paired">Paired</option>
142 <option value="Pastel1">Pastel1</option>
143 <option value="Pastel2">Pastel2</option>
144 <option value="Set1">Set1</option>
145 <option value="Set2">Set2</option>
146 <option value="Set3">Set3</option>
147 <option value="Vega10">Vega10</option>
148 <option value="Vega20">Vega20</option>
149 <option value="Vega20b">Vega20b</option>
150 <option value="Vega20c">Vega20c</option>
151 <option value="gist_earth">gist_earth</option>
152 <option value="terrain">terrain</option>
153 <option value="ocean">ocean</option>
154 <option value="gist_stern">gist_stern</option>
155 <option value="brg">brg</option>
156 <option value="CMRmap">CMRmap</option>
157 <option value="cubehelix">cubehelix</option>
158 <option value="gnuplot">gnuplot</option>
159 <option value="gnuplot2">gnuplot2</option>
160 <option value="gist_ncar">gist_ncar</option>
161 <option value="nipy_spectral">nipy_spectral</option>
162 <option value="jet">jet</option>
163 <option value="rainbow">rainbow</option>
164 <option value="gist_rainbow">gist_rainbow</option>
165 <option value="hsv">hsv</option>
166 <option value="flag">flag</option>
167 <option value="prism">prism</option>
168 </param>
169 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
170
171 </inputs>
172
173 <outputs>
174 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
175
176 </outputs>
177
178 <help><![CDATA[
179 Dendrogram heatmap.
180 ###############################################################
181
182 .. deprecated::
183 This Visualizer is deprecated and will be removed in a future version of
184 this plugin.
185
186 Visualize the feature table as a heatmap, with samples sorted along a
187 specified categorical metadata column and features clustered together
188 specified by the tree.
189
190 Parameters
191 ----------
192 table : FeatureTable[Frequency]
193 The feature table that will be plotted as a heatmap. This table is
194 assumed to have strictly positive values.
195 tree : Hierarchy
196 A hierarchy of feature identifiers where each tipcorresponds to the
197 feature identifiers in the table. This tree can contain tip ids that
198 are not present in the table, but all feature ids in the table must be
199 present in this tree.
200 metadata : MetadataColumn[Categorical]
201 Categorical metadata column to group the samples.
202 pseudocount : Float, optional
203 The pseudocount to add to avoid division by zero.
204 ndim : Int, optional
205 Number of dimensions to highlight.
206 method : Str % Choices('clr', 'log'), optional
207 Specifies how the data should be normalized for display.Options include
208 'log' or 'clr' (default='clr').
209 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
210 Specifies the color map for plotting the heatmap. See
211 https://matplotlib.org/examples/color/colormaps_reference.html for more
212 details.
213
214 Returns
215 -------
216 visualization : Visualization
217 ]]></help>
218 <macros>
219 <import>qiime_citation.xml</import>
220 </macros>
221 <expand macro="qiime_citation"/>
222 </tool>