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comparison qiime2/qiime_sample-classifier_heatmap.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_sample-classifier_heatmap" name="qiime sample-classifier heatmap" version="2019.4">
3 <description> - Generate heatmap of important features.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime sample-classifier heatmap
9
10 --i-table=$itable
11 --i-importance=$iimportance
12
13
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($input_files_mmetadatafile)
23 #end if
24
25
26
27 #if str($mmetadatacolumn):
28 --m-metadata-column="$mmetadatacolumn"
29 #end if
30
31 #if $pfeaturecount:
32 --p-feature-count=$pfeaturecount
33 #end if
34
35 #if $pimportancethreshold:
36 --p-importance-threshold=$pimportancethreshold
37 #end if
38
39 #if $pgroupsamples:
40 --p-group-samples
41 #end if
42
43 #if $pnonormalize:
44 --p-no-normalize
45 #end if
46
47 #if str($pmetric) != 'None':
48 --p-metric=$pmetric
49 #end if
50
51 #if str($pmethod) != 'None':
52 --p-method=$pmethod
53 #end if
54
55 #if str($pcluster) != 'None':
56 --p-cluster=$pcluster
57 #end if
58
59 #if str($pcolorscheme) != 'None':
60 --p-color-scheme=$pcolorscheme
61 #end if
62
63 --o-heatmap=oheatmap
64 --o-filtered-table=ofilteredtable
65 ;
66 qiime tools export --input-path oheatmap.qzv --output-path out && mkdir -p '$oheatmap.files_path'
67 && cp -r out/* '$oheatmap.files_path'
68 && mv '$oheatmap.files_path/index.html' '$oheatmap';
69 cp ofilteredtable.qza $ofilteredtable
70 ]]></command>
71 <inputs>
72 <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"/>
73 <param format="qza,no_unzip.zip" label="--i-importance: ARTIFACT FeatureData[Importance] Feature importances. [required]" name="iimportance" optional="False" type="data"/>
74 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Metadata file to convert to feature table. [optional]" name="mmetadatacolumn" optional="True" type="text"/>
75 <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]" name="pfeaturecount" optional="True" type="integer" value="50" min="0"/>
76 <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]" name="pimportancethreshold" optional="True" type="float" value="0" min="0"/>
77 <param label="--p-group-samples: --p-no-group-samples Group samples by metadata. [default: False]" name="pgroupsamples" selected="False" type="boolean"/>
78 <param label="--p-no-normalize: Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table. [default: False]" name="pnonormalize" selected="False" type="boolean"/>
79 <param label="--p-metric: " name="pmetric" optional="True" type="select">
80 <option selected="True" value="None">Selection is Optional</option>
81 <option value="kulsinski">kulsinski</option>
82 <option value="correlation">correlation</option>
83 <option value="hamming">hamming</option>
84 <option value="canberra">canberra</option>
85 <option value="sqeuclidean">sqeuclidean</option>
86 <option value="sokalmichener">sokalmichener</option>
87 <option value="cityblock">cityblock</option>
88 <option value="braycurtis">braycurtis</option>
89 <option value="matching">matching</option>
90 <option value="russellrao">russellrao</option>
91 <option value="cosine">cosine</option>
92 <option value="yule">yule</option>
93 <option value="minkowski">minkowski</option>
94 <option value="euclidean">euclidean</option>
95 <option value="rogerstanimoto">rogerstanimoto</option>
96 <option value="seuclidean">seuclidean</option>
97 <option value="jaccard">jaccard</option>
98 <option value="sokalsneath">sokalsneath</option>
99 <option value="chebyshev">chebyshev</option>
100 <option value="dice">dice</option>
101 <option value="mahalanobis">mahalanobis</option>
102 </param>
103 <param label="--p-method: " name="pmethod" optional="True" type="select">
104 <option selected="True" value="None">Selection is Optional</option>
105 <option value="complete">complete</option>
106 <option value="centroid">centroid</option>
107 <option value="weighted">weighted</option>
108 <option value="single">single</option>
109 <option value="ward">ward</option>
110 <option value="average">average</option>
111 <option value="median">median</option>
112 </param>
113 <param label="--p-cluster: " name="pcluster" optional="True" type="select">
114 <option selected="True" value="None">Selection is Optional</option>
115 <option value="features">features</option>
116 <option value="both">both</option>
117 <option value="samples">samples</option>
118 <option value="none">none</option>
119 </param>
120 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
121 <option selected="True" value="None">Selection is Optional</option>
122 <option value="bone">bone</option>
123 <option value="PRGn_r">PRGn_r</option>
124 <option value="Vega10_r">Vega10_r</option>
125 <option value="GnBu">GnBu</option>
126 <option value="hsv">hsv</option>
127 <option value="binary_r">binary_r</option>
128 <option value="GnBu_r">GnBu_r</option>
129 <option value="icefire">icefire</option>
130 <option value="winter">winter</option>
131 <option value="BuGn_r">BuGn_r</option>
132 <option value="plasma_r">plasma_r</option>
133 <option value="Vega20_r">Vega20_r</option>
134 <option value="summer_r">summer_r</option>
135 <option value="cool_r">cool_r</option>
136 <option value="Spectral">Spectral</option>
137 <option value="gist_heat_r">gist_heat_r</option>
138 <option value="Vega20b_r">Vega20b_r</option>
139 <option value="mako_r">mako_r</option>
140 <option value="RdBu_r">RdBu_r</option>
141 <option value="cubehelix">cubehelix</option>
142 <option value="tab20b_r">tab20b_r</option>
143 <option value="CMRmap">CMRmap</option>
144 <option value="Greys">Greys</option>
145 <option value="PuOr">PuOr</option>
146 <option value="cubehelix_r">cubehelix_r</option>
147 <option value="Wistia">Wistia</option>
148 <option value="gnuplot2">gnuplot2</option>
149 <option value="bwr">bwr</option>
150 <option value="gnuplot_r">gnuplot_r</option>
151 <option value="viridis">viridis</option>
152 <option value="gist_ncar_r">gist_ncar_r</option>
153 <option value="gist_ncar">gist_ncar</option>
154 <option value="plasma">plasma</option>
155 <option value="PuRd">PuRd</option>
156 <option value="afmhot">afmhot</option>
157 <option value="icefire_r">icefire_r</option>
158 <option value="tab20b">tab20b</option>
159 <option value="gist_yarg_r">gist_yarg_r</option>
160 <option value="hot">hot</option>
161 <option value="YlOrRd_r">YlOrRd_r</option>
162 <option value="Vega20c">Vega20c</option>
163 <option value="Dark2_r">Dark2_r</option>
164 <option value="Set3">Set3</option>
165 <option value="PuBu">PuBu</option>
166 <option value="magma">magma</option>
167 <option value="Pastel2">Pastel2</option>
168 <option value="terrain">terrain</option>
169 <option value="autumn_r">autumn_r</option>
170 <option value="spectral">spectral</option>
171 <option value="brg">brg</option>
172 <option value="Set3_r">Set3_r</option>
173 <option value="coolwarm">coolwarm</option>
174 <option value="Set2_r">Set2_r</option>
175 <option value="Paired_r">Paired_r</option>
176 <option value="tab20c_r">tab20c_r</option>
177 <option value="mako">mako</option>
178 <option value="gist_rainbow_r">gist_rainbow_r</option>
179 <option value="RdBu">RdBu</option>
180 <option value="PuBu_r">PuBu_r</option>
181 <option value="jet_r">jet_r</option>
182 <option value="gist_earth_r">gist_earth_r</option>
183 <option value="Greys_r">Greys_r</option>
184 <option value="gray">gray</option>
185 <option value="winter_r">winter_r</option>
186 <option value="rocket">rocket</option>
187 <option value="Set2">Set2</option>
188 <option value="seismic_r">seismic_r</option>
189 <option value="Pastel1">Pastel1</option>
190 <option value="RdYlGn_r">RdYlGn_r</option>
191 <option value="copper">copper</option>
192 <option value="spring_r">spring_r</option>
193 <option value="BuGn">BuGn</option>
194 <option value="Greens">Greens</option>
195 <option value="Blues">Blues</option>
196 <option value="PiYG_r">PiYG_r</option>
197 <option value="YlGnBu">YlGnBu</option>
198 <option value="Paired">Paired</option>
199 <option value="YlGn_r">YlGn_r</option>
200 <option value="RdPu_r">RdPu_r</option>
201 <option value="BrBG_r">BrBG_r</option>
202 <option value="bone_r">bone_r</option>
203 <option value="RdYlBu">RdYlBu</option>
204 <option value="gist_rainbow">gist_rainbow</option>
205 <option value="bwr_r">bwr_r</option>
206 <option value="inferno_r">inferno_r</option>
207 <option value="inferno">inferno</option>
208 <option value="gist_stern_r">gist_stern_r</option>
209 <option value="gray_r">gray_r</option>
210 <option value="Purples">Purples</option>
211 <option value="RdGy">RdGy</option>
212 <option value="hot_r">hot_r</option>
213 <option value="YlOrBr_r">YlOrBr_r</option>
214 <option value="nipy_spectral">nipy_spectral</option>
215 <option value="nipy_spectral_r">nipy_spectral_r</option>
216 <option value="ocean">ocean</option>
217 <option value="Set1">Set1</option>
218 <option value="Dark2">Dark2</option>
219 <option value="Oranges">Oranges</option>
220 <option value="Pastel1_r">Pastel1_r</option>
221 <option value="Oranges_r">Oranges_r</option>
222 <option value="Pastel2_r">Pastel2_r</option>
223 <option value="YlGn">YlGn</option>
224 <option value="Vega20b">Vega20b</option>
225 <option value="PuRd_r">PuRd_r</option>
226 <option value="PuBuGn_r">PuBuGn_r</option>
227 <option value="afmhot_r">afmhot_r</option>
228 <option value="spring">spring</option>
229 <option value="tab20_r">tab20_r</option>
230 <option value="PuBuGn">PuBuGn</option>
231 <option value="gist_yarg">gist_yarg</option>
232 <option value="PiYG">PiYG</option>
233 <option value="flag">flag</option>
234 <option value="rainbow_r">rainbow_r</option>
235 <option value="hsv_r">hsv_r</option>
236 <option value="prism_r">prism_r</option>
237 <option value="ocean_r">ocean_r</option>
238 <option value="magma_r">magma_r</option>
239 <option value="flag_r">flag_r</option>
240 <option value="Blues_r">Blues_r</option>
241 <option value="gnuplot2_r">gnuplot2_r</option>
242 <option value="gist_gray">gist_gray</option>
243 <option value="spectral_r">spectral_r</option>
244 <option value="CMRmap_r">CMRmap_r</option>
245 <option value="rainbow">rainbow</option>
246 <option value="gnuplot">gnuplot</option>
247 <option value="vlag">vlag</option>
248 <option value="Set1_r">Set1_r</option>
249 <option value="Accent">Accent</option>
250 <option value="coolwarm_r">coolwarm_r</option>
251 <option value="brg_r">brg_r</option>
252 <option value="pink_r">pink_r</option>
253 <option value="YlOrBr">YlOrBr</option>
254 <option value="Vega20c_r">Vega20c_r</option>
255 <option value="Wistia_r">Wistia_r</option>
256 <option value="RdGy_r">RdGy_r</option>
257 <option value="tab20">tab20</option>
258 <option value="BrBG">BrBG</option>
259 <option value="rocket_r">rocket_r</option>
260 <option value="OrRd_r">OrRd_r</option>
261 <option value="YlGnBu_r">YlGnBu_r</option>
262 <option value="viridis_r">viridis_r</option>
263 <option value="copper_r">copper_r</option>
264 <option value="gist_heat">gist_heat</option>
265 <option value="Vega10">Vega10</option>
266 <option value="PuOr_r">PuOr_r</option>
267 <option value="binary">binary</option>
268 <option value="pink">pink</option>
269 <option value="Reds">Reds</option>
270 <option value="Purples_r">Purples_r</option>
271 <option value="cool">cool</option>
272 <option value="prism">prism</option>
273 <option value="terrain_r">terrain_r</option>
274 <option value="BuPu_r">BuPu_r</option>
275 <option value="Spectral_r">Spectral_r</option>
276 <option value="Greens_r">Greens_r</option>
277 <option value="gist_gray_r">gist_gray_r</option>
278 <option value="RdYlGn">RdYlGn</option>
279 <option value="tab20c">tab20c</option>
280 <option value="Reds_r">Reds_r</option>
281 <option value="tab10">tab10</option>
282 <option value="summer">summer</option>
283 <option value="gist_stern">gist_stern</option>
284 <option value="tab10_r">tab10_r</option>
285 <option value="YlOrRd">YlOrRd</option>
286 <option value="jet">jet</option>
287 <option value="Vega20">Vega20</option>
288 <option value="vlag_r">vlag_r</option>
289 <option value="RdPu">RdPu</option>
290 <option value="OrRd">OrRd</option>
291 <option value="Accent_r">Accent_r</option>
292 <option value="autumn">autumn</option>
293 <option value="BuPu">BuPu</option>
294 <option value="RdYlBu_r">RdYlBu_r</option>
295 <option value="gist_earth">gist_earth</option>
296 <option value="seismic">seismic</option>
297 <option value="PRGn">PRGn</option>
298 </param>
299
300 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
301 <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" />
302 </repeat>
303
304 </inputs>
305 <outputs>
306 <data format="html" label="${tool.name} on ${on_string}: heatmap.qzv" name="oheatmap"/>
307 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/>
308 </outputs>
309 <help><![CDATA[
310 Generate heatmap of important features.
311 #######################################
312
313 Generate a heatmap of important features. Features are filtered based on
314 importance scores; samples are optionally grouped by metadata; and a
315 heatmap is generated that displays (normalized) feature abundances per
316 sample.
317
318 Parameters
319 ----------
320 table : FeatureTable[Frequency]
321 Feature table containing all features that should be used for target
322 prediction.
323 importance : FeatureData[Importance]
324 Feature importances.
325 metadata : MetadataColumn[Categorical], optional
326 Metadata file to convert to feature table.
327 feature_count : Int % Range(0, None), optional
328 Filter feature table to include top N most important features. Set to
329 zero to include all features.
330 importance_threshold : Float % Range(0, None), optional
331 Filter feature table to exclude any features with an importance score
332 less than this threshold. Set to zero to include all features.
333 group_samples : Bool, optional
334 Group samples by metadata.
335 normalize : Bool, optional
336 Normalize the feature table by adding a psuedocount of 1 and then
337 taking the log10 of the table.
338 metric : Str % Choices('sokalmichener', 'yule', 'russellrao', 'rogerstanimoto', 'minkowski', 'correlation', 'jaccard', 'cosine', 'chebyshev', 'euclidean', 'sqeuclidean', 'cityblock', 'matching', 'dice', 'mahalanobis', 'kulsinski', 'seuclidean', 'sokalsneath', 'canberra', 'hamming', 'braycurtis'), optional
339 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
340 born.clustermap.html#seaborn.clustermap for more detail).
341 method : Str % Choices('average', 'complete', 'median', 'centroid', 'single', 'ward', 'weighted'), optional
342 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
343 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
344 cluster : Str % Choices('features', 'samples', 'none', 'both'), optional
345 Specify which axes to cluster.
346 color_scheme : Str % Choices('rocket', 'RdYlBu_r', 'winter', 'viridis', 'BrBG', 'magma_r', 'YlOrBr', 'seismic', 'Set1', 'gist_yarg_r', 'gist_rainbow', 'autumn_r', 'Wistia_r', 'cool_r', 'hsv_r', 'flag', 'Vega20b_r', 'mako_r', 'coolwarm', 'Vega20_r', 'jet', 'cubehelix_r', 'bwr_r', 'brg', 'RdPu', 'gist_ncar', 'RdPu_r', 'cool', 'gnuplot_r', 'Set3', 'ocean_r', 'tab20b', 'tab20b_r', 'OrRd_r', 'Spectral_r', 'gray', 'OrRd', 'prism_r', 'Wistia', 'hot', 'icefire', 'plasma', 'Purples_r', 'viridis_r', 'gnuplot2_r', 'CMRmap', 'YlGnBu_r', 'Set3_r', 'PuRd_r', 'Reds_r', 'gray_r', 'Dark2', 'Vega20b', 'Paired', 'gist_yarg', 'RdYlGn_r', 'Greens', 'YlGnBu', 'tab20', 'gnuplot', 'PuBuGn_r', 'spectral_r', 'tab20c_r', 'gist_rainbow_r', 'hot_r', 'spring_r', 'gist_gray', 'Blues_r', 'Spectral', 'magma', 'GnBu_r', 'inferno_r', 'tab10', 'gist_gray_r', 'seismic_r', 'spring', 'BuPu_r', 'spectral', 'BrBG_r', 'PiYG', 'inferno', 'YlOrBr_r', 'Set1_r', 'YlOrRd_r', 'summer', 'vlag', 'Oranges_r', 'Dark2_r', 'binary_r', 'icefire_r', 'RdYlGn', 'hsv', 'gist_heat', 'PRGn_r', 'pink_r', 'Pastel2_r', 'copper_r', 'BuGn', 'gist_stern_r', 'PuRd', 'gist_earth_r', 'YlOrRd', 'Reds', 'gist_earth', 'Greens_r', 'Vega10', 'ocean', 'brg_r', 'rainbow_r', 'tab20_r', 'Purples', 'Blues', 'Accent', 'afmhot_r', 'Set2_r', 'RdBu', 'Vega20c', 'Pastel1', 'RdGy_r', 'PuBuGn', 'copper', 'PuOr', 'jet_r', 'YlGn_r', 'gist_heat_r', 'PuOr_r', 'bone', 'BuGn_r', 'terrain_r', 'mako', 'Vega20c_r', 'Paired_r', 'PuBu_r', 'tab20c', 'Pastel1_r', 'flag_r', 'plasma_r', 'Oranges', 'autumn', 'bone_r', 'GnBu', 'bwr', 'Greys', 'RdBu_r', 'RdGy', 'winter_r', 'gnuplot2', 'coolwarm_r', 'pink', 'nipy_spectral', 'Greys_r', 'summer_r', 'Vega20', 'BuPu', 'afmhot', 'gist_stern', 'binary', 'PiYG_r', 'YlGn', 'rocket_r', 'cubehelix', 'rainbow', 'Accent_r', 'CMRmap_r', 'PRGn', 'PuBu', 'tab10_r', 'prism', 'vlag_r', 'Set2', 'gist_ncar_r', 'nipy_spectral_r', 'Pastel2', 'terrain', 'RdYlBu', 'Vega10_r'), optional
347 Color scheme for heatmap.
348
349 Returns
350 -------
351 heatmap : Visualization
352 Heatmap of important features.
353 filtered_table : FeatureTable[Frequency]
354 Filtered feature table containing data displayed in heatmap.
355 ]]></help>
356 <macros>
357 <import>qiime_citation.xml</import>
358 </macros>
359 <expand macro="qiime_citation"/>
360 </tool>