Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_sample-classifier_heatmap.xml @ 20:d93d8888f0b0 draft
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| author | florianbegusch |
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| date | Fri, 04 Sep 2020 12:44:24 +0000 |
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| 19:6c48f8d82424 | 20:d93d8888f0b0 |
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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> |