Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_feature-table_heatmap.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | 51025741f326 |
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1 <?xml version="1.0" ?> | |
2 <tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap" version="2019.4"> | |
3 <description> - Generate a heatmap representation of a feature table</description> | |
4 <requirements> | |
5 <requirement type="package" version="2019.4">qiime2</requirement> | |
6 </requirements> | |
7 <command><![CDATA[ | |
8 qiime feature-table heatmap | |
9 | |
10 --i-table=$itable | |
11 | |
12 #if $input_files_mmetadatafile: | |
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-metadata-file=' + d['additional_input'].__getattr__('file_name') | |
17 #end for | |
18 #return $file_list | |
19 #end def | |
20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) | |
21 #end if | |
22 | |
23 | |
24 #if str($mmetadatacolumn): | |
25 --m-metadata-column="$mmetadatacolumn" | |
26 #end if | |
27 | |
28 #if $pnonormalize: | |
29 --p-no-normalize | |
30 #end if | |
31 | |
32 #if str($ptitle): | |
33 --p-title="$ptitle" | |
34 #end if | |
35 | |
36 #if str($pmetric) != 'None': | |
37 --p-metric=$pmetric | |
38 #end if | |
39 | |
40 #if str($pmethod) != 'None': | |
41 --p-method=$pmethod | |
42 #end if | |
43 | |
44 #if str($pcluster) != 'None': | |
45 --p-cluster=$pcluster | |
46 #end if | |
47 | |
48 #if str($pcolorscheme) != 'None': | |
49 --p-color-scheme=$pcolorscheme | |
50 #end if | |
51 | |
52 --o-visualization=ovisualization | |
53 ; | |
54 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' | |
55 && cp -r out/* '$ovisualization.files_path' | |
56 && mv '$ovisualization.files_path/index.html' '$ovisualization' | |
57 ]]></command> | |
58 <inputs> | |
59 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to visualize. [required]" name="itable" optional="False" type="data"/> | |
60 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Annotate the sample IDs with these metadata values. When metadata is present and `cluster`='feature', samples will be sorted by the metadata values. [optional]" name="mmetadatacolumn" optional="True" type="text"/> | |
61 <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: False]" name="pnonormalize" selected="False" type="boolean"/> | |
62 <param label="--p-title: TEXT Optional custom plot title. [optional]" name="ptitle" optional="True" type="text"/> | |
63 <param label="--p-metric: " name="pmetric" optional="True" type="select"> | |
64 <option selected="True" value="None">Selection is Optional</option> | |
65 <option value="kulsinski">kulsinski</option> | |
66 <option value="correlation">correlation</option> | |
67 <option value="hamming">hamming</option> | |
68 <option value="canberra">canberra</option> | |
69 <option value="sqeuclidean">sqeuclidean</option> | |
70 <option value="sokalmichener">sokalmichener</option> | |
71 <option value="cityblock">cityblock</option> | |
72 <option value="braycurtis">braycurtis</option> | |
73 <option value="matching">matching</option> | |
74 <option value="russellrao">russellrao</option> | |
75 <option value="cosine">cosine</option> | |
76 <option value="yule">yule</option> | |
77 <option value="minkowski">minkowski</option> | |
78 <option value="euclidean">euclidean</option> | |
79 <option value="rogerstanimoto">rogerstanimoto</option> | |
80 <option value="seuclidean">seuclidean</option> | |
81 <option value="jaccard">jaccard</option> | |
82 <option value="sokalsneath">sokalsneath</option> | |
83 <option value="chebyshev">chebyshev</option> | |
84 <option value="dice">dice</option> | |
85 <option value="mahalanobis">mahalanobis</option> | |
86 </param> | |
87 <param label="--p-method: " name="pmethod" optional="True" type="select"> | |
88 <option selected="True" value="None">Selection is Optional</option> | |
89 <option value="complete">complete</option> | |
90 <option value="centroid">centroid</option> | |
91 <option value="weighted">weighted</option> | |
92 <option value="single">single</option> | |
93 <option value="ward">ward</option> | |
94 <option value="average">average</option> | |
95 <option value="median">median</option> | |
96 </param> | |
97 <param label="--p-cluster: " name="pcluster" optional="True" type="select"> | |
98 <option selected="True" value="None">Selection is Optional</option> | |
99 <option value="features">features</option> | |
100 <option value="both">both</option> | |
101 <option value="samples">samples</option> | |
102 <option value="none">none</option> | |
103 </param> | |
104 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select"> | |
105 <option selected="True" value="None">Selection is Optional</option> | |
106 <option value="bone">bone</option> | |
107 <option value="PRGn_r">PRGn_r</option> | |
108 <option value="Vega10_r">Vega10_r</option> | |
109 <option value="GnBu">GnBu</option> | |
110 <option value="hsv">hsv</option> | |
111 <option value="binary_r">binary_r</option> | |
112 <option value="GnBu_r">GnBu_r</option> | |
113 <option value="icefire">icefire</option> | |
114 <option value="winter">winter</option> | |
115 <option value="BuGn_r">BuGn_r</option> | |
116 <option value="plasma_r">plasma_r</option> | |
117 <option value="Vega20_r">Vega20_r</option> | |
118 <option value="summer_r">summer_r</option> | |
119 <option value="cool_r">cool_r</option> | |
120 <option value="Spectral">Spectral</option> | |
121 <option value="gist_heat_r">gist_heat_r</option> | |
122 <option value="Vega20b_r">Vega20b_r</option> | |
123 <option value="mako_r">mako_r</option> | |
124 <option value="RdBu_r">RdBu_r</option> | |
125 <option value="cubehelix">cubehelix</option> | |
126 <option value="tab20b_r">tab20b_r</option> | |
127 <option value="CMRmap">CMRmap</option> | |
128 <option value="Greys">Greys</option> | |
129 <option value="PuOr">PuOr</option> | |
130 <option value="cubehelix_r">cubehelix_r</option> | |
131 <option value="Wistia">Wistia</option> | |
132 <option value="gnuplot2">gnuplot2</option> | |
133 <option value="bwr">bwr</option> | |
134 <option value="gnuplot_r">gnuplot_r</option> | |
135 <option value="viridis">viridis</option> | |
136 <option value="gist_ncar_r">gist_ncar_r</option> | |
137 <option value="gist_ncar">gist_ncar</option> | |
138 <option value="plasma">plasma</option> | |
139 <option value="PuRd">PuRd</option> | |
140 <option value="afmhot">afmhot</option> | |
141 <option value="icefire_r">icefire_r</option> | |
142 <option value="tab20b">tab20b</option> | |
143 <option value="gist_yarg_r">gist_yarg_r</option> | |
144 <option value="hot">hot</option> | |
145 <option value="YlOrRd_r">YlOrRd_r</option> | |
146 <option value="Vega20c">Vega20c</option> | |
147 <option value="Dark2_r">Dark2_r</option> | |
148 <option value="Set3">Set3</option> | |
149 <option value="PuBu">PuBu</option> | |
150 <option value="magma">magma</option> | |
151 <option value="Pastel2">Pastel2</option> | |
152 <option value="terrain">terrain</option> | |
153 <option value="autumn_r">autumn_r</option> | |
154 <option value="spectral">spectral</option> | |
155 <option value="brg">brg</option> | |
156 <option value="Set3_r">Set3_r</option> | |
157 <option value="coolwarm">coolwarm</option> | |
158 <option value="Set2_r">Set2_r</option> | |
159 <option value="Paired_r">Paired_r</option> | |
160 <option value="tab20c_r">tab20c_r</option> | |
161 <option value="mako">mako</option> | |
162 <option value="gist_rainbow_r">gist_rainbow_r</option> | |
163 <option value="RdBu">RdBu</option> | |
164 <option value="PuBu_r">PuBu_r</option> | |
165 <option value="jet_r">jet_r</option> | |
166 <option value="gist_earth_r">gist_earth_r</option> | |
167 <option value="Greys_r">Greys_r</option> | |
168 <option value="gray">gray</option> | |
169 <option value="winter_r">winter_r</option> | |
170 <option value="rocket">rocket</option> | |
171 <option value="Set2">Set2</option> | |
172 <option value="seismic_r">seismic_r</option> | |
173 <option value="Pastel1">Pastel1</option> | |
174 <option value="RdYlGn_r">RdYlGn_r</option> | |
175 <option value="copper">copper</option> | |
176 <option value="spring_r">spring_r</option> | |
177 <option value="BuGn">BuGn</option> | |
178 <option value="Greens">Greens</option> | |
179 <option value="Blues">Blues</option> | |
180 <option value="PiYG_r">PiYG_r</option> | |
181 <option value="YlGnBu">YlGnBu</option> | |
182 <option value="Paired">Paired</option> | |
183 <option value="YlGn_r">YlGn_r</option> | |
184 <option value="RdPu_r">RdPu_r</option> | |
185 <option value="BrBG_r">BrBG_r</option> | |
186 <option value="bone_r">bone_r</option> | |
187 <option value="RdYlBu">RdYlBu</option> | |
188 <option value="gist_rainbow">gist_rainbow</option> | |
189 <option value="bwr_r">bwr_r</option> | |
190 <option value="inferno_r">inferno_r</option> | |
191 <option value="inferno">inferno</option> | |
192 <option value="gist_stern_r">gist_stern_r</option> | |
193 <option value="gray_r">gray_r</option> | |
194 <option value="Purples">Purples</option> | |
195 <option value="RdGy">RdGy</option> | |
196 <option value="hot_r">hot_r</option> | |
197 <option value="YlOrBr_r">YlOrBr_r</option> | |
198 <option value="nipy_spectral">nipy_spectral</option> | |
199 <option value="nipy_spectral_r">nipy_spectral_r</option> | |
200 <option value="ocean">ocean</option> | |
201 <option value="Set1">Set1</option> | |
202 <option value="Dark2">Dark2</option> | |
203 <option value="Oranges">Oranges</option> | |
204 <option value="Pastel1_r">Pastel1_r</option> | |
205 <option value="Oranges_r">Oranges_r</option> | |
206 <option value="Pastel2_r">Pastel2_r</option> | |
207 <option value="YlGn">YlGn</option> | |
208 <option value="Vega20b">Vega20b</option> | |
209 <option value="PuRd_r">PuRd_r</option> | |
210 <option value="PuBuGn_r">PuBuGn_r</option> | |
211 <option value="afmhot_r">afmhot_r</option> | |
212 <option value="spring">spring</option> | |
213 <option value="tab20_r">tab20_r</option> | |
214 <option value="PuBuGn">PuBuGn</option> | |
215 <option value="gist_yarg">gist_yarg</option> | |
216 <option value="PiYG">PiYG</option> | |
217 <option value="flag">flag</option> | |
218 <option value="rainbow_r">rainbow_r</option> | |
219 <option value="hsv_r">hsv_r</option> | |
220 <option value="prism_r">prism_r</option> | |
221 <option value="ocean_r">ocean_r</option> | |
222 <option value="magma_r">magma_r</option> | |
223 <option value="flag_r">flag_r</option> | |
224 <option value="Blues_r">Blues_r</option> | |
225 <option value="gnuplot2_r">gnuplot2_r</option> | |
226 <option value="gist_gray">gist_gray</option> | |
227 <option value="spectral_r">spectral_r</option> | |
228 <option value="CMRmap_r">CMRmap_r</option> | |
229 <option value="rainbow">rainbow</option> | |
230 <option value="gnuplot">gnuplot</option> | |
231 <option value="vlag">vlag</option> | |
232 <option value="Set1_r">Set1_r</option> | |
233 <option value="Accent">Accent</option> | |
234 <option value="coolwarm_r">coolwarm_r</option> | |
235 <option value="brg_r">brg_r</option> | |
236 <option value="pink_r">pink_r</option> | |
237 <option value="YlOrBr">YlOrBr</option> | |
238 <option value="Vega20c_r">Vega20c_r</option> | |
239 <option value="Wistia_r">Wistia_r</option> | |
240 <option value="RdGy_r">RdGy_r</option> | |
241 <option value="tab20">tab20</option> | |
242 <option value="BrBG">BrBG</option> | |
243 <option value="rocket_r">rocket_r</option> | |
244 <option value="OrRd_r">OrRd_r</option> | |
245 <option value="YlGnBu_r">YlGnBu_r</option> | |
246 <option value="viridis_r">viridis_r</option> | |
247 <option value="copper_r">copper_r</option> | |
248 <option value="gist_heat">gist_heat</option> | |
249 <option value="Vega10">Vega10</option> | |
250 <option value="PuOr_r">PuOr_r</option> | |
251 <option value="binary">binary</option> | |
252 <option value="pink">pink</option> | |
253 <option value="Reds">Reds</option> | |
254 <option value="Purples_r">Purples_r</option> | |
255 <option value="cool">cool</option> | |
256 <option value="prism">prism</option> | |
257 <option value="terrain_r">terrain_r</option> | |
258 <option value="BuPu_r">BuPu_r</option> | |
259 <option value="Spectral_r">Spectral_r</option> | |
260 <option value="Greens_r">Greens_r</option> | |
261 <option value="gist_gray_r">gist_gray_r</option> | |
262 <option value="RdYlGn">RdYlGn</option> | |
263 <option value="tab20c">tab20c</option> | |
264 <option value="Reds_r">Reds_r</option> | |
265 <option value="tab10">tab10</option> | |
266 <option value="summer">summer</option> | |
267 <option value="gist_stern">gist_stern</option> | |
268 <option value="tab10_r">tab10_r</option> | |
269 <option value="YlOrRd">YlOrRd</option> | |
270 <option value="jet">jet</option> | |
271 <option value="Vega20">Vega20</option> | |
272 <option value="vlag_r">vlag_r</option> | |
273 <option value="RdPu">RdPu</option> | |
274 <option value="OrRd">OrRd</option> | |
275 <option value="Accent_r">Accent_r</option> | |
276 <option value="autumn">autumn</option> | |
277 <option value="BuPu">BuPu</option> | |
278 <option value="RdYlBu_r">RdYlBu_r</option> | |
279 <option value="gist_earth">gist_earth</option> | |
280 <option value="seismic">seismic</option> | |
281 <option value="PRGn">PRGn</option> | |
282 </param> | |
283 | |
284 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file"> | |
285 <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" /> | |
286 </repeat> | |
287 </inputs> | |
288 <outputs> | |
289 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> | |
290 </outputs> | |
291 <help><![CDATA[ | |
292 Generate a heatmap representation of a feature table | |
293 #################################################### | |
294 | |
295 Generate a heatmap representation of a feature table with optional | |
296 clustering on both the sample and feature axes. Tip: To generate a heatmap | |
297 containing taxonomic annotations, use `qiime taxa collapse` to collapse the | |
298 feature table at the desired taxonomic level. | |
299 | |
300 Parameters | |
301 ---------- | |
302 table : FeatureTable[Frequency] | |
303 The feature table to visualize. | |
304 metadata : MetadataColumn[Categorical], optional | |
305 Annotate the sample IDs with these metadata values. When metadata is | |
306 present and \`cluster\`='feature', samples will be sorted by the metadata | |
307 values. | |
308 normalize : Bool, optional | |
309 Normalize the feature table by adding a psuedocount of 1 and then | |
310 taking the log10 of the table. | |
311 title : Str, optional | |
312 Optional custom plot title. | |
313 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 | |
314 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea | |
315 born.clustermap.html#seaborn.clustermap for more detail). | |
316 method : Str % Choices('average', 'complete', 'median', 'centroid', 'single', 'ward', 'weighted'), optional | |
317 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge | |
318 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail). | |
319 cluster : Str % Choices('features', 'samples', 'none', 'both'), optional | |
320 Specify which axes to cluster. | |
321 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 | |
322 The matplotlib colorscheme to generate the heatmap with. | |
323 | |
324 Returns | |
325 ------- | |
326 visualization : Visualization | |
327 ]]></help> | |
328 <macros> | |
329 <import>qiime_citation.xml</import> | |
330 </macros> | |
331 <expand macro="qiime_citation"/> | |
332 </tool> |