Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2-2020.8/qiime_feature-table_heatmap.xml @ 20:d93d8888f0b0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
parents
children
comparison
equal deleted inserted replaced
19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap"
3 version="2020.8">
4 <description>Generate a heatmap representation of a feature table</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime feature-table heatmap
10
11 --i-table=$itable
12 # if $input_files_msamplemetadatafile:
13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
21 # end if
22
23 #if '__ob__' in str($msamplemetadatacolumn):
24 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__ob__', '[')
25 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
26 #end if
27 #if '__cb__' in str($msamplemetadatacolumn):
28 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__cb__', ']')
29 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
30 #end if
31 #if 'X' in str($msamplemetadatacolumn):
32 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('X', '\\')
33 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
34 #end if
35 #if '__sq__' in str($msamplemetadatacolumn):
36 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__sq__', "'")
37 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
38 #end if
39 #if '__db__' in str($msamplemetadatacolumn):
40 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__db__', '"')
41 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
42 #end if
43
44 #if str($msamplemetadatacolumn):
45 --m-sample-metadata-column=$msamplemetadatacolumn
46 #end if
47 # if $input_files_mfeaturemetadatafile:
48 # def list_dict_to_string(list_dict):
49 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
50 # for d in list_dict[1:]:
51 # set $file_list = $file_list + ' --m-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
52 # end for
53 # return $file_list
54 # end def
55 --m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
56 # end if
57
58 #if '__ob__' in str($mfeaturemetadatacolumn):
59 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__ob__', '[')
60 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
61 #end if
62 #if '__cb__' in str($mfeaturemetadatacolumn):
63 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__cb__', ']')
64 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
65 #end if
66 #if 'X' in str($mfeaturemetadatacolumn):
67 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('X', '\\')
68 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
69 #end if
70 #if '__sq__' in str($mfeaturemetadatacolumn):
71 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__sq__', "'")
72 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
73 #end if
74 #if '__db__' in str($mfeaturemetadatacolumn):
75 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__db__', '"')
76 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
77 #end if
78
79 #if str($mfeaturemetadatacolumn):
80 --m-feature-metadata-column=$mfeaturemetadatacolumn
81 #end if
82
83 #if $pnonormalize:
84 --p-no-normalize
85 #end if
86
87 #if str($ptitle):
88 --p-title=$ptitle
89 #end if
90 #if str($pmetric) != 'None':
91 --p-metric=$pmetric
92 #end if
93
94 #if str($pmethod) != 'None':
95 --p-method=$pmethod
96 #end if
97
98 #if str($pcluster) != 'None':
99 --p-cluster=$pcluster
100 #end if
101
102 #if str($pcolorscheme) != 'None':
103 --p-color-scheme=$pcolorscheme
104 #end if
105
106 --o-visualization=ovisualization
107
108 #if str($examples) != 'None':
109 --examples=$examples
110 #end if
111
112 ;
113 cp ogroupedtable.qza $ogroupedtable
114
115 ;
116 qiime tools export ovisualization.qzv --output-path out
117 && mkdir -p '$ovisualization.files_path'
118 && cp -r out/* '$ovisualization.files_path'
119 && mv '$ovisualization.files_path/index.html' '$ovisualization'
120
121 ]]></command>
122 <inputs>
123 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to visualize. [required]" name="itable" optional="False" type="data" />
124 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
125 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
126 </repeat>
127 <param label="--m-sample-metadata-column: COLUMN MetadataColumn[Categorical] Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`=\'feature\', samples will be sorted by the metadata values. [optional]" name="msamplemetadatacolumn" optional="False" type="text" />
128 <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
129 <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
130 </repeat>
131 <param label="--m-feature-metadata-column: COLUMN MetadataColumn[Categorical] Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`=\'sample\', features will be sorted by the metadata values. [optional]" name="mfeaturemetadatacolumn" optional="False" type="text" />
132 <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" />
133 <param label="--p-title: TEXT Optional custom plot title. [optional]" name="ptitle" optional="False" type="text" />
134 <param label="--p-metric: " name="pmetric" optional="True" type="select">
135 <option selected="True" value="None">Selection is Optional</option>
136 <option value="euclidean">euclidean</option>
137 <option value="cityblock">cityblock</option>
138 <option value="matching">matching</option>
139 <option value="russellrao">russellrao</option>
140 <option value="sokalmichener">sokalmichener</option>
141 <option value="kulsinski">kulsinski</option>
142 <option value="chebyshev">chebyshev</option>
143 <option value="hamming">hamming</option>
144 <option value="dice">dice</option>
145 <option value="yule">yule</option>
146 <option value="rogerstanimoto">rogerstanimoto</option>
147 <option value="braycurtis">braycurtis</option>
148 <option value="cosine">cosine</option>
149 <option value="minkowski">minkowski</option>
150 <option value="correlation">correlation</option>
151 <option value="sokalsneath">sokalsneath</option>
152 <option value="seuclidean">seuclidean</option>
153 <option value="canberra">canberra</option>
154 <option value="mahalanobis">mahalanobis</option>
155 <option value="jaccard">jaccard</option>
156 <option value="sqeuclidean">sqeuclidean</option>
157 </param>
158 <param label="--p-method: " name="pmethod" optional="True" type="select">
159 <option selected="True" value="None">Selection is Optional</option>
160 <option value="centroid">centroid</option>
161 <option value="median">median</option>
162 <option value="weighted">weighted</option>
163 <option value="average">average</option>
164 <option value="single">single</option>
165 <option value="complete">complete</option>
166 <option value="ward">ward</option>
167 </param>
168 <param label="--p-cluster: " name="pcluster" optional="True" type="select">
169 <option selected="True" value="None">Selection is Optional</option>
170 <option value="both">both</option>
171 <option value="none">none</option>
172 <option value="features">features</option>
173 <option value="samples">samples</option>
174 </param>
175 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
176 <option selected="True" value="None">Selection is Optional</option>
177 <option value="Spectral">Spectral</option>
178 <option value="flag">flag</option>
179 <option value="jet">jet</option>
180 <option value="Vega20">Vega20</option>
181 <option value="terrain">terrain</option>
182 <option value="jet_r">jet_r</option>
183 <option value="Vega20c_r">Vega20c_r</option>
184 <option value="Oranges_r">Oranges_r</option>
185 <option value="spectral">spectral</option>
186 <option value="summer">summer</option>
187 <option value="BuPu_r">BuPu_r</option>
188 <option value="tab20b_r">tab20b_r</option>
189 <option value="Pastel1">Pastel1</option>
190 <option value="gnuplot_r">gnuplot_r</option>
191 <option value="seismic">seismic</option>
192 <option value="icefire">icefire</option>
193 <option value="Set1">Set1</option>
194 <option value="bwr">bwr</option>
195 <option value="coolwarm_r">coolwarm_r</option>
196 <option value="ocean_r">ocean_r</option>
197 <option value="gist_gray_r">gist_gray_r</option>
198 <option value="autumn">autumn</option>
199 <option value="BrBG">BrBG</option>
200 <option value="Pastel2">Pastel2</option>
201 <option value="GnBu">GnBu</option>
202 <option value="Vega20b_r">Vega20b_r</option>
203 <option value="tab20c">tab20c</option>
204 <option value="Paired">Paired</option>
205 <option value="YlOrRd_r">YlOrRd_r</option>
206 <option value="icefire_r">icefire_r</option>
207 <option value="cubehelix_r">cubehelix_r</option>
208 <option value="CMRmap_r">CMRmap_r</option>
209 <option value="RdBu">RdBu</option>
210 <option value="YlGn_r">YlGn_r</option>
211 <option value="gray_r">gray_r</option>
212 <option value="mako_r">mako_r</option>
213 <option value="OrRd_r">OrRd_r</option>
214 <option value="Vega10">Vega10</option>
215 <option value="Set3">Set3</option>
216 <option value="RdYlGn_r">RdYlGn_r</option>
217 <option value="hsv">hsv</option>
218 <option value="cool_r">cool_r</option>
219 <option value="Spectral_r">Spectral_r</option>
220 <option value="rainbow">rainbow</option>
221 <option value="cividis">cividis</option>
222 <option value="Blues_r">Blues_r</option>
223 <option value="PuOr_r">PuOr_r</option>
224 <option value="binary_r">binary_r</option>
225 <option value="RdGy">RdGy</option>
226 <option value="Pastel2_r">Pastel2_r</option>
227 <option value="Pastel1_r">Pastel1_r</option>
228 <option value="Dark2">Dark2</option>
229 <option value="vlag">vlag</option>
230 <option value="binary">binary</option>
231 <option value="pink">pink</option>
232 <option value="Purples">Purples</option>
233 <option value="cividis_r">cividis_r</option>
234 <option value="gray">gray</option>
235 <option value="seismic_r">seismic_r</option>
236 <option value="Greys">Greys</option>
237 <option value="tab20">tab20</option>
238 <option value="BuPu">BuPu</option>
239 <option value="RdBu_r">RdBu_r</option>
240 <option value="gnuplot2_r">gnuplot2_r</option>
241 <option value="Accent_r">Accent_r</option>
242 <option value="magma">magma</option>
243 <option value="copper_r">copper_r</option>
244 <option value="inferno">inferno</option>
245 <option value="nipy_spectral_r">nipy_spectral_r</option>
246 <option value="pink_r">pink_r</option>
247 <option value="copper">copper</option>
248 <option value="Dark2_r">Dark2_r</option>
249 <option value="YlGnBu_r">YlGnBu_r</option>
250 <option value="Wistia_r">Wistia_r</option>
251 <option value="spectral_r">spectral_r</option>
252 <option value="cubehelix">cubehelix</option>
253 <option value="tab20_r">tab20_r</option>
254 <option value="viridis">viridis</option>
255 <option value="RdYlBu">RdYlBu</option>
256 <option value="Blues">Blues</option>
257 <option value="rocket_r">rocket_r</option>
258 <option value="Set1_r">Set1_r</option>
259 <option value="brg_r">brg_r</option>
260 <option value="bone_r">bone_r</option>
261 <option value="gist_ncar_r">gist_ncar_r</option>
262 <option value="afmhot">afmhot</option>
263 <option value="RdYlBu_r">RdYlBu_r</option>
264 <option value="gist_earth_r">gist_earth_r</option>
265 <option value="RdGy_r">RdGy_r</option>
266 <option value="Vega10_r">Vega10_r</option>
267 <option value="gist_rainbow_r">gist_rainbow_r</option>
268 <option value="spring">spring</option>
269 <option value="Set3_r">Set3_r</option>
270 <option value="magma_r">magma_r</option>
271 <option value="mako">mako</option>
272 <option value="PuRd">PuRd</option>
273 <option value="gnuplot2">gnuplot2</option>
274 <option value="Paired_r">Paired_r</option>
275 <option value="Vega20b">Vega20b</option>
276 <option value="Accent">Accent</option>
277 <option value="hsv_r">hsv_r</option>
278 <option value="ocean">ocean</option>
279 <option value="gist_earth">gist_earth</option>
280 <option value="afmhot_r">afmhot_r</option>
281 <option value="bone">bone</option>
282 <option value="rocket">rocket</option>
283 <option value="RdYlGn">RdYlGn</option>
284 <option value="bwr_r">bwr_r</option>
285 <option value="RdPu_r">RdPu_r</option>
286 <option value="BuGn">BuGn</option>
287 <option value="PuBu">PuBu</option>
288 <option value="hot_r">hot_r</option>
289 <option value="Vega20c">Vega20c</option>
290 <option value="gist_yarg">gist_yarg</option>
291 <option value="tab10">tab10</option>
292 <option value="coolwarm">coolwarm</option>
293 <option value="winter_r">winter_r</option>
294 <option value="plasma_r">plasma_r</option>
295 <option value="Wistia">Wistia</option>
296 <option value="BuGn_r">BuGn_r</option>
297 <option value="Set2">Set2</option>
298 <option value="Vega20_r">Vega20_r</option>
299 <option value="hot">hot</option>
300 <option value="brg">brg</option>
301 <option value="BrBG_r">BrBG_r</option>
302 <option value="gist_heat">gist_heat</option>
303 <option value="YlOrRd">YlOrRd</option>
304 <option value="inferno_r">inferno_r</option>
305 <option value="viridis_r">viridis_r</option>
306 <option value="gist_stern_r">gist_stern_r</option>
307 <option value="tab20c_r">tab20c_r</option>
308 <option value="gist_gray">gist_gray</option>
309 <option value="Reds_r">Reds_r</option>
310 <option value="flag_r">flag_r</option>
311 <option value="Purples_r">Purples_r</option>
312 <option value="vlag_r">vlag_r</option>
313 <option value="summer_r">summer_r</option>
314 <option value="Greys_r">Greys_r</option>
315 <option value="PRGn">PRGn</option>
316 <option value="PiYG">PiYG</option>
317 <option value="gist_ncar">gist_ncar</option>
318 <option value="Oranges">Oranges</option>
319 <option value="Reds">Reds</option>
320 <option value="GnBu_r">GnBu_r</option>
321 <option value="RdPu">RdPu</option>
322 <option value="YlOrBr_r">YlOrBr_r</option>
323 <option value="autumn_r">autumn_r</option>
324 <option value="YlGn">YlGn</option>
325 <option value="CMRmap">CMRmap</option>
326 <option value="gnuplot">gnuplot</option>
327 <option value="rainbow_r">rainbow_r</option>
328 <option value="PiYG_r">PiYG_r</option>
329 <option value="Greens">Greens</option>
330 <option value="YlOrBr">YlOrBr</option>
331 <option value="prism_r">prism_r</option>
332 <option value="winter">winter</option>
333 <option value="gist_yarg_r">gist_yarg_r</option>
334 <option value="Set2_r">Set2_r</option>
335 <option value="nipy_spectral">nipy_spectral</option>
336 <option value="plasma">plasma</option>
337 <option value="OrRd">OrRd</option>
338 <option value="Greens_r">Greens_r</option>
339 <option value="tab10_r">tab10_r</option>
340 <option value="YlGnBu">YlGnBu</option>
341 <option value="prism">prism</option>
342 <option value="PRGn_r">PRGn_r</option>
343 <option value="gist_heat_r">gist_heat_r</option>
344 <option value="terrain_r">terrain_r</option>
345 <option value="tab20b">tab20b</option>
346 <option value="PuBuGn">PuBuGn</option>
347 <option value="PuBu_r">PuBu_r</option>
348 <option value="spring_r">spring_r</option>
349 <option value="gist_rainbow">gist_rainbow</option>
350 <option value="cool">cool</option>
351 <option value="PuOr">PuOr</option>
352 <option value="PuRd_r">PuRd_r</option>
353 <option value="gist_stern">gist_stern</option>
354 <option value="PuBuGn_r">PuBuGn_r</option>
355 </param>
356 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
357
358 </inputs>
359
360 <outputs>
361 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
362
363 </outputs>
364
365 <help><![CDATA[
366 Generate a heatmap representation of a feature table
367 ###############################################################
368
369 Generate a heatmap representation of a feature table with optional
370 clustering on both the sample and feature axes. Tip: To generate a heatmap
371 containing taxonomic annotations, use `qiime taxa collapse` to collapse the
372 feature table at the desired taxonomic level.
373
374 Parameters
375 ----------
376 table : FeatureTable[Frequency]
377 The feature table to visualize.
378 sample_metadata : MetadataColumn[Categorical], optional
379 Annotate the sample IDs with these sample metadata values. When
380 metadata is present and `cluster`='feature', samples will be sorted by
381 the metadata values.
382 feature_metadata : MetadataColumn[Categorical], optional
383 Annotate the feature IDs with these feature metadata values. When
384 metadata is present and `cluster`='sample', features will be sorted by
385 the metadata values.
386 normalize : Bool, optional
387 Normalize the feature table by adding a psuedocount of 1 and then
388 taking the log10 of the table.
389 title : Str, optional
390 Optional custom plot title.
391 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
392 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
393 born.clustermap.html#seaborn.clustermap for more detail).
394 method : Str % Choices('complete', 'average', 'ward', 'median', 'weighted', 'centroid', 'single'), optional
395 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
396 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
397 cluster : Str % Choices('both', 'features', 'none', 'samples'), optional
398 Specify which axes to cluster.
399 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
400 The matplotlib colorscheme to generate the heatmap with.
401
402 Returns
403 -------
404 visualization : Visualization
405 ]]></help>
406 <macros>
407 <import>qiime_citation.xml</import>
408 </macros>
409 <expand macro="qiime_citation"/>
410 </tool>