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comparison qiime2-2020.8/qiime_sample-classifier_heatmap.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_sample-classifier_heatmap" name="qiime sample-classifier heatmap"
3 version="2020.8">
4 <description>Generate heatmap of important features.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime sample-classifier heatmap
10
11 --i-table=$itable
12
13 --i-importance=$iimportance
14 # if $input_files_msamplemetadatafile:
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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
19 # end for
20 # return $file_list
21 # end def
22 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
23 # end if
24
25 #if '__ob__' in str($msamplemetadatacolumn):
26 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__ob__', '[')
27 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
28 #end if
29 #if '__cb__' in str($msamplemetadatacolumn):
30 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__cb__', ']')
31 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
32 #end if
33 #if 'X' in str($msamplemetadatacolumn):
34 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('X', '\\')
35 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
36 #end if
37 #if '__sq__' in str($msamplemetadatacolumn):
38 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__sq__', "'")
39 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
40 #end if
41 #if '__db__' in str($msamplemetadatacolumn):
42 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__db__', '"')
43 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
44 #end if
45
46 #if str($msamplemetadatacolumn):
47 --m-sample-metadata-column=$msamplemetadatacolumn
48 #end if
49 # if $input_files_mfeaturemetadatafile:
50 # def list_dict_to_string(list_dict):
51 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
52 # for d in list_dict[1:]:
53 # set $file_list = $file_list + ' --m-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
54 # end for
55 # return $file_list
56 # end def
57 --m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
58 # end if
59
60 #if '__ob__' in str($mfeaturemetadatacolumn):
61 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__ob__', '[')
62 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
63 #end if
64 #if '__cb__' in str($mfeaturemetadatacolumn):
65 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__cb__', ']')
66 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
67 #end if
68 #if 'X' in str($mfeaturemetadatacolumn):
69 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('X', '\\')
70 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
71 #end if
72 #if '__sq__' in str($mfeaturemetadatacolumn):
73 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__sq__', "'")
74 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
75 #end if
76 #if '__db__' in str($mfeaturemetadatacolumn):
77 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__db__', '"')
78 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
79 #end if
80
81 #if str($mfeaturemetadatacolumn):
82 --m-feature-metadata-column=$mfeaturemetadatacolumn
83 #end if
84
85 --p-feature-count=$pfeaturecount
86
87 --p-importance-threshold=$pimportancethreshold
88
89 #if $pgroupsamples:
90 --p-group-samples
91 #end if
92
93 #if $pnonormalize:
94 --p-no-normalize
95 #end if
96
97 #if str($pmissingsamples) != 'None':
98 --p-missing-samples=$pmissingsamples
99 #end if
100
101 #if str($pmetric) != 'None':
102 --p-metric=$pmetric
103 #end if
104
105 #if str($pmethod) != 'None':
106 --p-method=$pmethod
107 #end if
108
109 #if str($pcluster) != 'None':
110 --p-cluster=$pcluster
111 #end if
112
113 #if str($pcolorscheme) != 'None':
114 --p-color-scheme=$pcolorscheme
115 #end if
116
117 --o-heatmap=oheatmap
118
119 --o-filtered-table=ofilteredtable
120
121 #if str($examples) != 'None':
122 --examples=$examples
123 #end if
124
125 ;
126 cp ofilteredtable.qza $ofilteredtable
127
128 ]]></command>
129 <inputs>
130 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [required]" name="itable" optional="False" type="data" />
131 <param format="qza,no_unzip.zip" label="--i-importance: ARTIFACT FeatureData[Importance] Feature importances. [required]" name="iimportance" optional="False" type="data" />
132 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
133 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
134 </repeat>
135 <param label="--m-sample-metadata-column: COLUMN MetadataColumn[Categorical] Sample metadata column to use for sample labeling or grouping. [optional]" name="msamplemetadatacolumn" optional="False" type="text" />
136 <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
137 <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
138 </repeat>
139 <param label="--m-feature-metadata-column: COLUMN MetadataColumn[Categorical] Feature metadata (e.g., taxonomy) to use for labeling features in the heatmap. [optional]" name="mfeaturemetadatacolumn" optional="False" type="text" />
140 <param label="--p-feature-count: INTEGER Range(0, None) Filter feature table to include top N most important features. Set to zero to include all features. [default: 50]" min="0" name="pfeaturecount" optional="True" type="integer" value="50" />
141 <param label="--p-importance-threshold: NUMBER Range(0, None) Filter feature table to exclude any features with an importance score less than this threshold. Set to zero to include all features. [default: 0]" min="0" name="pimportancethreshold" optional="True" type="integer" value="0" />
142 <param label="--p-group-samples: --p-group-samples: / --p-no-group-samples Group samples by sample metadata. [default: False]" name="pgroupsamples" selected="False" type="boolean" />
143 <param label="--p-no-normalize: Do not normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table. [default: True]" name="pnonormalize" selected="False" type="boolean" />
144 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
145 <option selected="True" value="None">Selection is Optional</option>
146 <option value="error">error</option>
147 <option value="ignore">ignore</option>
148 </param>
149 <param label="--p-metric: " name="pmetric" optional="True" type="select">
150 <option selected="True" value="None">Selection is Optional</option>
151 <option value="euclidean">euclidean</option>
152 <option value="cityblock">cityblock</option>
153 <option value="matching">matching</option>
154 <option value="russellrao">russellrao</option>
155 <option value="sokalmichener">sokalmichener</option>
156 <option value="kulsinski">kulsinski</option>
157 <option value="chebyshev">chebyshev</option>
158 <option value="hamming">hamming</option>
159 <option value="dice">dice</option>
160 <option value="yule">yule</option>
161 <option value="rogerstanimoto">rogerstanimoto</option>
162 <option value="braycurtis">braycurtis</option>
163 <option value="cosine">cosine</option>
164 <option value="minkowski">minkowski</option>
165 <option value="correlation">correlation</option>
166 <option value="sokalsneath">sokalsneath</option>
167 <option value="seuclidean">seuclidean</option>
168 <option value="canberra">canberra</option>
169 <option value="mahalanobis">mahalanobis</option>
170 <option value="jaccard">jaccard</option>
171 <option value="sqeuclidean">sqeuclidean</option>
172 </param>
173 <param label="--p-method: " name="pmethod" optional="True" type="select">
174 <option selected="True" value="None">Selection is Optional</option>
175 <option value="centroid">centroid</option>
176 <option value="median">median</option>
177 <option value="weighted">weighted</option>
178 <option value="average">average</option>
179 <option value="single">single</option>
180 <option value="complete">complete</option>
181 <option value="ward">ward</option>
182 </param>
183 <param label="--p-cluster: " name="pcluster" optional="True" type="select">
184 <option selected="True" value="None">Selection is Optional</option>
185 <option value="both">both</option>
186 <option value="none">none</option>
187 <option value="features">features</option>
188 <option value="samples">samples</option>
189 </param>
190 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
191 <option selected="True" value="None">Selection is Optional</option>
192 <option value="Spectral">Spectral</option>
193 <option value="flag">flag</option>
194 <option value="jet">jet</option>
195 <option value="Vega20">Vega20</option>
196 <option value="terrain">terrain</option>
197 <option value="jet_r">jet_r</option>
198 <option value="Vega20c_r">Vega20c_r</option>
199 <option value="Oranges_r">Oranges_r</option>
200 <option value="spectral">spectral</option>
201 <option value="summer">summer</option>
202 <option value="BuPu_r">BuPu_r</option>
203 <option value="tab20b_r">tab20b_r</option>
204 <option value="Pastel1">Pastel1</option>
205 <option value="gnuplot_r">gnuplot_r</option>
206 <option value="seismic">seismic</option>
207 <option value="icefire">icefire</option>
208 <option value="Set1">Set1</option>
209 <option value="bwr">bwr</option>
210 <option value="coolwarm_r">coolwarm_r</option>
211 <option value="ocean_r">ocean_r</option>
212 <option value="gist_gray_r">gist_gray_r</option>
213 <option value="autumn">autumn</option>
214 <option value="BrBG">BrBG</option>
215 <option value="Pastel2">Pastel2</option>
216 <option value="GnBu">GnBu</option>
217 <option value="Vega20b_r">Vega20b_r</option>
218 <option value="tab20c">tab20c</option>
219 <option value="Paired">Paired</option>
220 <option value="YlOrRd_r">YlOrRd_r</option>
221 <option value="icefire_r">icefire_r</option>
222 <option value="cubehelix_r">cubehelix_r</option>
223 <option value="CMRmap_r">CMRmap_r</option>
224 <option value="RdBu">RdBu</option>
225 <option value="YlGn_r">YlGn_r</option>
226 <option value="gray_r">gray_r</option>
227 <option value="mako_r">mako_r</option>
228 <option value="OrRd_r">OrRd_r</option>
229 <option value="Vega10">Vega10</option>
230 <option value="Set3">Set3</option>
231 <option value="RdYlGn_r">RdYlGn_r</option>
232 <option value="hsv">hsv</option>
233 <option value="cool_r">cool_r</option>
234 <option value="Spectral_r">Spectral_r</option>
235 <option value="rainbow">rainbow</option>
236 <option value="cividis">cividis</option>
237 <option value="Blues_r">Blues_r</option>
238 <option value="PuOr_r">PuOr_r</option>
239 <option value="binary_r">binary_r</option>
240 <option value="RdGy">RdGy</option>
241 <option value="Pastel2_r">Pastel2_r</option>
242 <option value="Pastel1_r">Pastel1_r</option>
243 <option value="Dark2">Dark2</option>
244 <option value="vlag">vlag</option>
245 <option value="binary">binary</option>
246 <option value="pink">pink</option>
247 <option value="Purples">Purples</option>
248 <option value="cividis_r">cividis_r</option>
249 <option value="gray">gray</option>
250 <option value="seismic_r">seismic_r</option>
251 <option value="Greys">Greys</option>
252 <option value="tab20">tab20</option>
253 <option value="BuPu">BuPu</option>
254 <option value="RdBu_r">RdBu_r</option>
255 <option value="gnuplot2_r">gnuplot2_r</option>
256 <option value="Accent_r">Accent_r</option>
257 <option value="magma">magma</option>
258 <option value="copper_r">copper_r</option>
259 <option value="inferno">inferno</option>
260 <option value="nipy_spectral_r">nipy_spectral_r</option>
261 <option value="pink_r">pink_r</option>
262 <option value="copper">copper</option>
263 <option value="Dark2_r">Dark2_r</option>
264 <option value="YlGnBu_r">YlGnBu_r</option>
265 <option value="Wistia_r">Wistia_r</option>
266 <option value="spectral_r">spectral_r</option>
267 <option value="cubehelix">cubehelix</option>
268 <option value="tab20_r">tab20_r</option>
269 <option value="viridis">viridis</option>
270 <option value="RdYlBu">RdYlBu</option>
271 <option value="Blues">Blues</option>
272 <option value="rocket_r">rocket_r</option>
273 <option value="Set1_r">Set1_r</option>
274 <option value="brg_r">brg_r</option>
275 <option value="bone_r">bone_r</option>
276 <option value="gist_ncar_r">gist_ncar_r</option>
277 <option value="afmhot">afmhot</option>
278 <option value="RdYlBu_r">RdYlBu_r</option>
279 <option value="gist_earth_r">gist_earth_r</option>
280 <option value="RdGy_r">RdGy_r</option>
281 <option value="Vega10_r">Vega10_r</option>
282 <option value="gist_rainbow_r">gist_rainbow_r</option>
283 <option value="spring">spring</option>
284 <option value="Set3_r">Set3_r</option>
285 <option value="magma_r">magma_r</option>
286 <option value="mako">mako</option>
287 <option value="PuRd">PuRd</option>
288 <option value="gnuplot2">gnuplot2</option>
289 <option value="Paired_r">Paired_r</option>
290 <option value="Vega20b">Vega20b</option>
291 <option value="Accent">Accent</option>
292 <option value="hsv_r">hsv_r</option>
293 <option value="ocean">ocean</option>
294 <option value="gist_earth">gist_earth</option>
295 <option value="afmhot_r">afmhot_r</option>
296 <option value="bone">bone</option>
297 <option value="rocket">rocket</option>
298 <option value="RdYlGn">RdYlGn</option>
299 <option value="bwr_r">bwr_r</option>
300 <option value="RdPu_r">RdPu_r</option>
301 <option value="BuGn">BuGn</option>
302 <option value="PuBu">PuBu</option>
303 <option value="hot_r">hot_r</option>
304 <option value="Vega20c">Vega20c</option>
305 <option value="gist_yarg">gist_yarg</option>
306 <option value="tab10">tab10</option>
307 <option value="coolwarm">coolwarm</option>
308 <option value="winter_r">winter_r</option>
309 <option value="plasma_r">plasma_r</option>
310 <option value="Wistia">Wistia</option>
311 <option value="BuGn_r">BuGn_r</option>
312 <option value="Set2">Set2</option>
313 <option value="Vega20_r">Vega20_r</option>
314 <option value="hot">hot</option>
315 <option value="brg">brg</option>
316 <option value="BrBG_r">BrBG_r</option>
317 <option value="gist_heat">gist_heat</option>
318 <option value="YlOrRd">YlOrRd</option>
319 <option value="inferno_r">inferno_r</option>
320 <option value="viridis_r">viridis_r</option>
321 <option value="gist_stern_r">gist_stern_r</option>
322 <option value="tab20c_r">tab20c_r</option>
323 <option value="gist_gray">gist_gray</option>
324 <option value="Reds_r">Reds_r</option>
325 <option value="flag_r">flag_r</option>
326 <option value="Purples_r">Purples_r</option>
327 <option value="vlag_r">vlag_r</option>
328 <option value="summer_r">summer_r</option>
329 <option value="Greys_r">Greys_r</option>
330 <option value="PRGn">PRGn</option>
331 <option value="PiYG">PiYG</option>
332 <option value="gist_ncar">gist_ncar</option>
333 <option value="Oranges">Oranges</option>
334 <option value="Reds">Reds</option>
335 <option value="GnBu_r">GnBu_r</option>
336 <option value="RdPu">RdPu</option>
337 <option value="YlOrBr_r">YlOrBr_r</option>
338 <option value="autumn_r">autumn_r</option>
339 <option value="YlGn">YlGn</option>
340 <option value="CMRmap">CMRmap</option>
341 <option value="gnuplot">gnuplot</option>
342 <option value="rainbow_r">rainbow_r</option>
343 <option value="PiYG_r">PiYG_r</option>
344 <option value="Greens">Greens</option>
345 <option value="YlOrBr">YlOrBr</option>
346 <option value="prism_r">prism_r</option>
347 <option value="winter">winter</option>
348 <option value="gist_yarg_r">gist_yarg_r</option>
349 <option value="Set2_r">Set2_r</option>
350 <option value="nipy_spectral">nipy_spectral</option>
351 <option value="plasma">plasma</option>
352 <option value="OrRd">OrRd</option>
353 <option value="Greens_r">Greens_r</option>
354 <option value="tab10_r">tab10_r</option>
355 <option value="YlGnBu">YlGnBu</option>
356 <option value="prism">prism</option>
357 <option value="PRGn_r">PRGn_r</option>
358 <option value="gist_heat_r">gist_heat_r</option>
359 <option value="terrain_r">terrain_r</option>
360 <option value="tab20b">tab20b</option>
361 <option value="PuBuGn">PuBuGn</option>
362 <option value="PuBu_r">PuBu_r</option>
363 <option value="spring_r">spring_r</option>
364 <option value="gist_rainbow">gist_rainbow</option>
365 <option value="cool">cool</option>
366 <option value="PuOr">PuOr</option>
367 <option value="PuRd_r">PuRd_r</option>
368 <option value="gist_stern">gist_stern</option>
369 <option value="PuBuGn_r">PuBuGn_r</option>
370 </param>
371 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
372
373 </inputs>
374
375 <outputs>
376 <data format="html" label="${tool.name} on ${on_string}: heatmap.html" name="oheatmap" />
377 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
378
379 </outputs>
380
381 <help><![CDATA[
382 Generate heatmap of important features.
383 ###############################################################
384
385 Generate a heatmap of important features. Features are filtered based on
386 importance scores; samples are optionally grouped by sample metadata; and a
387 heatmap is generated that displays (normalized) feature abundances per
388 sample.
389
390 Parameters
391 ----------
392 table : FeatureTable[Frequency]
393 Feature table containing all features that should be used for target
394 prediction.
395 importance : FeatureData[Importance]
396 Feature importances.
397 sample_metadata : MetadataColumn[Categorical], optional
398 Sample metadata column to use for sample labeling or grouping.
399 feature_metadata : MetadataColumn[Categorical], optional
400 Feature metadata (e.g., taxonomy) to use for labeling features in the
401 heatmap.
402 feature_count : Int % Range(0, None), optional
403 Filter feature table to include top N most important features. Set to
404 zero to include all features.
405 importance_threshold : Float % Range(0, None), optional
406 Filter feature table to exclude any features with an importance score
407 less than this threshold. Set to zero to include all features.
408 group_samples : Bool, optional
409 Group samples by sample metadata.
410 normalize : Bool, optional
411 Normalize the feature table by adding a psuedocount of 1 and then
412 taking the log10 of the table.
413 missing_samples : Str % Choices('error', 'ignore'), optional
414 How to handle missing samples in metadata. "error" will fail if missing
415 samples are detected. "ignore" will cause the feature table and
416 metadata to be filtered, so that only samples found in both files are
417 retained.
418 metric : Str % Choices('yule', 'seuclidean', 'sokalmichener', 'sokalsneath', 'hamming', 'canberra', 'cityblock', 'russellrao', 'jaccard', 'braycurtis', 'minkowski', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'correlation', 'dice', 'rogerstanimoto', 'mahalanobis', 'chebyshev', 'matching'), optional
419 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
420 born.clustermap.html#seaborn.clustermap for more detail).
421 method : Str % Choices('complete', 'average', 'ward', 'median', 'weighted', 'centroid', 'single'), optional
422 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
423 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
424 cluster : Str % Choices('both', 'features', 'none', 'samples'), optional
425 Specify which axes to cluster.
426 color_scheme : Str % Choices('YlGn', 'flag', 'Greens_r', 'RdPu_r', 'OrRd', 'Set1_r', 'RdYlGn', 'inferno_r', 'Accent_r', 'bwr', 'PuOr', 'seismic_r', 'RdGy_r', 'tab20b_r', 'Oranges', 'spectral', 'RdYlGn_r', 'nipy_spectral_r', 'gist_gray', 'binary', 'gist_yarg_r', 'cubehelix', 'viridis_r', 'autumn', 'bone_r', 'terrain_r', 'RdPu', 'inferno', 'PRGn', 'YlGnBu', 'mako', 'gray', 'tab20_r', 'Oranges_r', 'gist_stern_r', 'Dark2_r', 'Purples_r', 'coolwarm', 'RdYlBu', 'tab10', 'copper_r', 'YlOrRd_r', 'gray_r', 'magma', 'Set3_r', 'BuGn', 'viridis', 'icefire_r', 'PuOr_r', 'YlOrBr', 'winter_r', 'hsv', 'gist_earth_r', 'rocket_r', 'Vega20b', 'autumn_r', 'gnuplot', 'Paired', 'PuRd_r', 'BrBG_r', 'plasma_r', 'Set2', 'prism', 'winter', 'seismic', 'RdGy', 'Blues_r', 'Reds_r', 'gist_ncar_r', 'Reds', 'afmhot', 'Greys', 'rainbow', 'tab10_r', 'GnBu_r', 'gnuplot2', 'pink', 'tab20b', 'BuGn_r', 'PuRd', 'gist_stern', 'magma_r', 'prism_r', 'tab20c_r', 'BuPu', 'cividis_r', 'BrBG', 'Wistia_r', 'gist_gray_r', 'ocean_r', 'summer_r', 'mako_r', 'CMRmap_r', 'cool_r', 'coolwarm_r', 'Greens', 'RdBu', 'icefire', 'spectral_r', 'Vega20', 'brg', 'Paired_r', 'BuPu_r', 'gist_rainbow', 'CMRmap', 'cool', 'gist_earth', 'bwr_r', 'rocket', 'YlGn_r', 'Vega20b_r', 'Wistia', 'Vega20c_r', 'Accent', 'plasma', 'Set1', 'PuBu_r', 'Purples', 'RdYlBu_r', 'brg_r', 'flag_r', 'Set3', 'hot_r', 'Blues', 'Pastel1_r', 'YlOrBr_r', 'hsv_r', 'Pastel2', 'Pastel1', 'bone', 'tab20', 'PuBuGn_r', 'terrain', 'gist_rainbow_r', 'Spectral_r', 'Pastel2_r', 'RdBu_r', 'summer', 'gist_ncar', 'OrRd_r', 'copper', 'tab20c', 'PuBuGn', 'Set2_r', 'vlag', 'jet_r', 'gist_heat_r', 'PRGn_r', 'Vega10', 'jet', 'Spectral', 'rainbow_r', 'binary_r', 'ocean', 'spring', 'Dark2', 'Vega20_r', 'vlag_r', 'PiYG', 'PuBu', 'YlGnBu_r', 'afmhot_r', 'nipy_spectral', 'gnuplot2_r', 'cividis', 'gnuplot_r', 'Greys_r', 'cubehelix_r', 'spring_r', 'PiYG_r', 'gist_yarg', 'gist_heat', 'Vega20c', 'GnBu', 'YlOrRd', 'hot', 'Vega10_r', 'pink_r'), optional
427 Color scheme for heatmap.
428
429 Returns
430 -------
431 heatmap : Visualization
432 Heatmap of important features.
433 filtered_table : FeatureTable[Frequency]
434 Filtered feature table containing data displayed in heatmap.
435 ]]></help>
436 <macros>
437 <import>qiime_citation.xml</import>
438 </macros>
439 <expand macro="qiime_citation"/>
440 </tool>