0
+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap" version="2018.4">
+ − 3 <description> - Generate a heatmap representation of a feature table</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2018.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command>
+ − 8 <![CDATA[
+ − 9 qiime feature-table heatmap --i-table=$itable
+ − 10
+ − 11 #if str($pcluster) != 'None':
+ − 12 --p-cluster=$pcluster
+ − 13 #end if
+ − 14
+ − 15 #if $input_files_mmetadatafile:
+ − 16
+ − 17 #def list_dict_to_string(list_dict):
+ − 18 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+ − 19 #for d in list_dict[1:]:
+ − 20 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
+ − 21 #end for
+ − 22 #return $file_list
+ − 23 #end def
+ − 24 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+ − 25 #end if
+ − 26
+ − 27 #if str($cmdconfig) != 'None':
+ − 28 --cmd-config=$cmdconfig
+ − 29 #end if
+ − 30 --o-visualization=ovisualization
+ − 31 #if str($mmetadatacolumn):
+ − 32 --m-metadata-column="$mmetadatacolumn"
+ − 33 #end if
+ − 34
+ − 35 #if $pnormalize:
+ − 36 --p-normalize
+ − 37 #else
+ − 38 --p-no-normalize
+ − 39 #end if
+ − 40
+ − 41 #if str($pmetric) != 'None':
+ − 42 --p-metric=$pmetric
+ − 43 #end if
+ − 44
+ − 45 #if str($ptitle):
+ − 46 --p-title="$ptitle"
+ − 47 #end if
+ − 48
+ − 49 #if str($pcolorscheme) != 'None':
+ − 50 --p-color-scheme=$pcolorscheme
+ − 51 #end if
+ − 52
+ − 53 #if str($pmethod) != 'None':
+ − 54 --p-method=$pmethod
+ − 55 #end if
+ − 56 ;
+ − 57 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
+ − 58 && cp -r out/* '$ovisualization.files_path'
+ − 59 && mv '$ovisualization.files_path/index.html' '$ovisualization'
+ − 60 ]]>
+ − 61 </command>
+ − 62 <inputs>
+ − 63 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to visualize. [required]" name="itable" optional="False" type="data"/>
+ − 64
+ − 65 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+ − 66 <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" />
+ − 67 </repeat>
+ − 68 <param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. 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"/>
+ − 69
+ − 70 <param label="--p-normalize: --p-no-normalize Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table. [default: True]" name="pnormalize" checked="True" type="boolean"/>
+ − 71 <param label="--p-title: Optional custom plot title. [optional]" name="ptitle" optional="True" type="text"/>
+ − 72
+ − 73 <param label="--p-metric: Metrics exposed by seaborn (see http://seabo
+ − 74 rn.pydata.org/generated/seaborn.clustermap.h
+ − 75 tml#seaborn.clustermap for more detail).
+ − 76 [default: euclidean]" name="pmetric" optional="True" type="select">
+ − 77 <option selected="True" value="None">Selection is Optional</option>
+ − 78 <option value="hamming">hamming</option>
+ − 79 <option value="sqeuclidean">sqeuclidean</option>
+ − 80 <option value="cityblock">cityblock</option>
+ − 81 <option value="sokalmichener">sokalmichener</option>
+ − 82 <option value="braycurtis">braycurtis</option>
+ − 83 <option value="cosine">cosine</option>
+ − 84 <option value="euclidean">euclidean</option>
+ − 85 <option value="rogerstanimoto">rogerstanimoto</option>
+ − 86 <option value="seuclidean">seuclidean</option>
+ − 87 <option value="canberra">canberra</option>
+ − 88 <option value="correlation">correlation</option>
+ − 89 <option value="sokalsneath">sokalsneath</option>
+ − 90 <option value="chebyshev">chebyshev</option>
+ − 91 <option value="mahalanobis">mahalanobis</option>
+ − 92 <option value="kulsinski">kulsinski</option>
+ − 93 <option value="matching">matching</option>
+ − 94 <option value="yule">yule</option>
+ − 95 <option value="dice">dice</option>
+ − 96 <option value="minkowski">minkowski</option>
+ − 97 <option value="russellrao">russellrao</option>
+ − 98 <option value="jaccard">jaccard</option>
+ − 99 </param>
+ − 100
+ − 101 <param label="--p-method: Clustering methods exposed by seaborn (see h
+ − 102 ttp://seaborn.pydata.org/generated/seaborn.c
+ − 103 lustermap.html#seaborn.clustermap for more
+ − 104 detail). [default: average]" name="pmethod" optional="True" type="select">
+ − 105 <option selected="True" value="None">Selection is Optional</option>
+ − 106 <option value="median">median</option>
+ − 107 <option value="average">average</option>
+ − 108 <option value="weighted">weighted</option>
+ − 109 <option value="ward">ward</option>
+ − 110 <option value="centroid">centroid</option>
+ − 111 <option value="single">single</option>
+ − 112 <option value="complete">complete</option>
+ − 113 </param>
+ − 114
+ − 115 <param label="--p-cluster: Specify which axes to cluster. [default:
+ − 116 both]" name="pcluster" optional="True" type="select">
+ − 117 <option selected="True" value="None">Selection is Optional</option>
+ − 118 <option value="samples">samples</option>
+ − 119 <option value="both">both</option>
+ − 120 <option value="features">features</option>
+ − 121 </param>
+ − 122
+ − 123
+ − 124 <param label="--p-color-scheme: The matplotlib colorscheme to generate the
+ − 125 heatmap with. [default: rocket]" name="pcolorscheme" optional="True" type="select">
+ − 126 <option selected="True" value="None">Selection is Optional</option>
+ − 127 <option value="gist_rainbow_r">gist_rainbow_r</option>
+ − 128 <option value="Purples_r">Purples_r</option>
+ − 129 <option value="plasma">plasma</option>
+ − 130 <option value="magma_r">magma_r</option>
+ − 131 <option value="Blues_r">Blues_r</option>
+ − 132 <option value="Set3_r">Set3_r</option>
+ − 133 <option value="terrain_r">terrain_r</option>
+ − 134 <option value="summer">summer</option>
+ − 135 <option value="gist_yarg">gist_yarg</option>
+ − 136 <option value="BrBG">BrBG</option>
+ − 137 <option value="Paired">Paired</option>
+ − 138 <option value="Vega10_r">Vega10_r</option>
+ − 139 <option value="binary">binary</option>
+ − 140 <option value="jet_r">jet_r</option>
+ − 141 <option value="magma">magma</option>
+ − 142 <option value="Spectral">Spectral</option>
+ − 143 <option value="prism_r">prism_r</option>
+ − 144 <option value="gist_ncar_r">gist_ncar_r</option>
+ − 145 <option value="ocean">ocean</option>
+ − 146 <option value="RdGy_r">RdGy_r</option>
+ − 147 <option value="Dark2">Dark2</option>
+ − 148 <option value="RdBu">RdBu</option>
+ − 149 <option value="gnuplot2">gnuplot2</option>
+ − 150 <option value="PuBuGn_r">PuBuGn_r</option>
+ − 151 <option value="OrRd">OrRd</option>
+ − 152 <option value="RdYlGn_r">RdYlGn_r</option>
+ − 153 <option value="gist_rainbow">gist_rainbow</option>
+ − 154 <option value="RdBu_r">RdBu_r</option>
+ − 155 <option value="BuPu">BuPu</option>
+ − 156 <option value="PuOr_r">PuOr_r</option>
+ − 157 <option value="Vega20c">Vega20c</option>
+ − 158 <option value="hot">hot</option>
+ − 159 <option value="OrRd_r">OrRd_r</option>
+ − 160 <option value="viridis">viridis</option>
+ − 161 <option value="cool_r">cool_r</option>
+ − 162 <option value="Accent_r">Accent_r</option>
+ − 163 <option value="gist_earth_r">gist_earth_r</option>
+ − 164 <option value="gist_gray_r">gist_gray_r</option>
+ − 165 <option value="Wistia">Wistia</option>
+ − 166 <option value="YlOrRd_r">YlOrRd_r</option>
+ − 167 <option value="Greys">Greys</option>
+ − 168 <option value="YlOrRd">YlOrRd</option>
+ − 169 <option value="gist_yarg_r">gist_yarg_r</option>
+ − 170 <option value="spring_r">spring_r</option>
+ − 171 <option value="YlGn">YlGn</option>
+ − 172 <option value="inferno">inferno</option>
+ − 173 <option value="YlGnBu">YlGnBu</option>
+ − 174 <option value="copper_r">copper_r</option>
+ − 175 <option value="tab20c_r">tab20c_r</option>
+ − 176 <option value="gist_heat_r">gist_heat_r</option>
+ − 177 <option value="Oranges_r">Oranges_r</option>
+ − 178 <option value="YlGn_r">YlGn_r</option>
+ − 179 <option value="PuBu">PuBu</option>
+ − 180 <option value="YlOrBr">YlOrBr</option>
+ − 181 <option value="icefire_r">icefire_r</option>
+ − 182 <option value="GnBu">GnBu</option>
+ − 183 <option value="nipy_spectral_r">nipy_spectral_r</option>
+ − 184 <option value="brg_r">brg_r</option>
+ − 185 <option value="seismic">seismic</option>
+ − 186 <option value="terrain">terrain</option>
+ − 187 <option value="gnuplot_r">gnuplot_r</option>
+ − 188 <option value="PuRd_r">PuRd_r</option>
+ − 189 <option value="RdYlGn">RdYlGn</option>
+ − 190 <option value="rainbow">rainbow</option>
+ − 191 <option value="vlag">vlag</option>
+ − 192 <option value="cubehelix_r">cubehelix_r</option>
+ − 193 <option value="mako_r">mako_r</option>
+ − 194 <option value="BuGn_r">BuGn_r</option>
+ − 195 <option value="BuPu_r">BuPu_r</option>
+ − 196 <option value="Set3">Set3</option>
+ − 197 <option value="gist_gray">gist_gray</option>
+ − 198 <option value="tab10">tab10</option>
+ − 199 <option value="YlOrBr_r">YlOrBr_r</option>
+ − 200 <option value="PRGn">PRGn</option>
+ − 201 <option value="Purples">Purples</option>
+ − 202 <option value="bwr">bwr</option>
+ − 203 <option value="tab20">tab20</option>
+ − 204 <option value="afmhot">afmhot</option>
+ − 205 <option value="spring">spring</option>
+ − 206 <option value="Set2_r">Set2_r</option>
+ − 207 <option value="spectral">spectral</option>
+ − 208 <option value="mako">mako</option>
+ − 209 <option value="seismic_r">seismic_r</option>
+ − 210 <option value="YlGnBu_r">YlGnBu_r</option>
+ − 211 <option value="cubehelix">cubehelix</option>
+ − 212 <option value="gray">gray</option>
+ − 213 <option value="Vega20b_r">Vega20b_r</option>
+ − 214 <option value="gist_stern">gist_stern</option>
+ − 215 <option value="gist_heat">gist_heat</option>
+ − 216 <option value="plasma_r">plasma_r</option>
+ − 217 <option value="Wistia_r">Wistia_r</option>
+ − 218 <option value="Set1_r">Set1_r</option>
+ − 219 <option value="gnuplot2_r">gnuplot2_r</option>
+ − 220 <option value="icefire">icefire</option>
+ − 221 <option value="inferno_r">inferno_r</option>
+ − 222 <option value="Pastel2_r">Pastel2_r</option>
+ − 223 <option value="Vega10">Vega10</option>
+ − 224 <option value="brg">brg</option>
+ − 225 <option value="Greens_r">Greens_r</option>
+ − 226 <option value="hsv_r">hsv_r</option>
+ − 227 <option value="PuOr">PuOr</option>
+ − 228 <option value="Reds">Reds</option>
+ − 229 <option value="prism">prism</option>
+ − 230 <option value="Pastel1_r">Pastel1_r</option>
+ − 231 <option value="Vega20">Vega20</option>
+ − 232 <option value="tab10_r">tab10_r</option>
+ − 233 <option value="PiYG_r">PiYG_r</option>
+ − 234 <option value="Accent">Accent</option>
+ − 235 <option value="tab20c">tab20c</option>
+ − 236 <option value="coolwarm">coolwarm</option>
+ − 237 <option value="gist_ncar">gist_ncar</option>
+ − 238 <option value="CMRmap">CMRmap</option>
+ − 239 <option value="Vega20_r">Vega20_r</option>
+ − 240 <option value="RdYlBu_r">RdYlBu_r</option>
+ − 241 <option value="vlag_r">vlag_r</option>
+ − 242 <option value="RdGy">RdGy</option>
+ − 243 <option value="gist_earth">gist_earth</option>
+ − 244 <option value="PuBuGn">PuBuGn</option>
+ − 245 <option value="bone_r">bone_r</option>
+ − 246 <option value="afmhot_r">afmhot_r</option>
+ − 247 <option value="CMRmap_r">CMRmap_r</option>
+ − 248 <option value="RdPu">RdPu</option>
+ − 249 <option value="RdYlBu">RdYlBu</option>
+ − 250 <option value="rocket_r">rocket_r</option>
+ − 251 <option value="cool">cool</option>
+ − 252 <option value="Blues">Blues</option>
+ − 253 <option value="flag_r">flag_r</option>
+ − 254 <option value="PuBu_r">PuBu_r</option>
+ − 255 <option value="jet">jet</option>
+ − 256 <option value="tab20b">tab20b</option>
+ − 257 <option value="PiYG">PiYG</option>
+ − 258 <option value="Greys_r">Greys_r</option>
+ − 259 <option value="Pastel2">Pastel2</option>
+ − 260 <option value="GnBu_r">GnBu_r</option>
+ − 261 <option value="coolwarm_r">coolwarm_r</option>
+ − 262 <option value="gray_r">gray_r</option>
+ − 263 <option value="tab20_r">tab20_r</option>
+ − 264 <option value="nipy_spectral">nipy_spectral</option>
+ − 265 <option value="bone">bone</option>
+ − 266 <option value="hsv">hsv</option>
+ − 267 <option value="RdPu_r">RdPu_r</option>
+ − 268 <option value="Set1">Set1</option>
+ − 269 <option value="ocean_r">ocean_r</option>
+ − 270 <option value="rainbow_r">rainbow_r</option>
+ − 271 <option value="BrBG_r">BrBG_r</option>
+ − 272 <option value="pink_r">pink_r</option>
+ − 273 <option value="bwr_r">bwr_r</option>
+ − 274 <option value="PuRd">PuRd</option>
+ − 275 <option value="Set2">Set2</option>
+ − 276 <option value="flag">flag</option>
+ − 277 <option value="gnuplot">gnuplot</option>
+ − 278 <option value="Paired_r">Paired_r</option>
+ − 279 <option value="Spectral_r">Spectral_r</option>
+ − 280 <option value="Pastel1">Pastel1</option>
+ − 281 <option value="spectral_r">spectral_r</option>
+ − 282 <option value="tab20b_r">tab20b_r</option>
+ − 283 <option value="autumn_r">autumn_r</option>
+ − 284 <option value="pink">pink</option>
+ − 285 <option value="gist_stern_r">gist_stern_r</option>
+ − 286 <option value="winter_r">winter_r</option>
+ − 287 <option value="PRGn_r">PRGn_r</option>
+ − 288 <option value="Vega20b">Vega20b</option>
+ − 289 <option value="winter">winter</option>
+ − 290 <option value="binary_r">binary_r</option>
+ − 291 <option value="Reds_r">Reds_r</option>
+ − 292 <option value="Greens">Greens</option>
+ − 293 <option value="autumn">autumn</option>
+ − 294 <option value="summer_r">summer_r</option>
+ − 295 <option value="BuGn">BuGn</option>
+ − 296 <option value="Vega20c_r">Vega20c_r</option>
+ − 297 <option value="viridis_r">viridis_r</option>
+ − 298 <option value="rocket">rocket</option>
+ − 299 <option value="hot_r">hot_r</option>
+ − 300 <option value="Dark2_r">Dark2_r</option>
+ − 301 <option value="Oranges">Oranges</option>
+ − 302 <option value="copper">copper</option>
+ − 303 </param>
+ − 304
+ − 305 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+ − 306 </inputs>
+ − 307 <outputs>
+ − 308 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+ − 309 </outputs>
+ − 310 <help>
+ − 311 <![CDATA[
+ − 312 Generate a heatmap representation of a feature table
+ − 313 -----------------------------------------------------
+ − 314
+ − 315 Generate a heatmap representation of a feature table with optional
+ − 316 clustering on both the sample and feature axes. Tip: To generate a heatmap
+ − 317 containing taxonomic annotations, use `qiime taxa collapse` to collapse the
+ − 318 feature table at the desired taxonomic level.
+ − 319
+ − 320 Parameters
+ − 321 ----------
+ − 322 table : FeatureTable[Frequency]
+ − 323 The feature table to visualize.
+ − 324 metadata : MetadataColumn[Categorical], optional
+ − 325 Annotate the sample IDs with these metadata values. When metadata is
+ − 326 present and `cluster`='feature', samples will be sorted by the metadata values.
+ − 327 normalize : Bool, optional
+ − 328 Normalize the feature table by adding a psuedocount of 1 and then
+ − 329 taking the log10 of the table.
+ − 330 title : Str, optional
+ − 331 Optional custom plot title.
+ − 332 metric : Str % Choices({'braycurtis', 'canberra', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'hamming', 'jaccard', 'kulsinski', 'mahalanobis', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'yule'}), optional
+ − 333 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
+ − 334 born.clustermap.html#seaborn.clustermap for more detail).
+ − 335 method : Str % Choices({'average', 'centroid', 'complete', 'median', 'single', 'ward', 'weighted'}), optional
+ − 336 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
+ − 337 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
+ − 338 cluster : Str % Choices({'both', 'features', 'samples'}), optional
+ − 339 Specify which axes to cluster.
+ − 340 color_scheme : Str % Choices({'Accent', 'Accent_r', 'Blues', 'Blues_r', 'BrBG', 'BrBG_r', 'BuGn', 'BuGn_r', 'BuPu', 'BuPu_r', 'CMRmap', 'CMRmap_r', 'Dark2', 'Dark2_r', 'GnBu', 'GnBu_r', 'Greens', 'Greens_r', 'Greys', 'Greys_r', 'OrRd', 'OrRd_r', 'Oranges', 'Oranges_r', 'PRGn', 'PRGn_r', 'Paired', 'Paired_r', 'Pastel1', 'Pastel1_r', 'Pastel2', 'Pastel2_r', 'PiYG', 'PiYG_r', 'PuBu', 'PuBuGn', 'PuBuGn_r', 'PuBu_r', 'PuOr', 'PuOr_r', 'PuRd', 'PuRd_r', 'Purples', 'Purples_r', 'RdBu', 'RdBu_r', 'RdGy', 'RdGy_r', 'RdPu', 'RdPu_r', 'RdYlBu', 'RdYlBu_r', 'RdYlGn', 'RdYlGn_r', 'Reds', 'Reds_r', 'Set1', 'Set1_r', 'Set2', 'Set2_r', 'Set3', 'Set3_r', 'Spectral', 'Spectral_r', 'Vega10', 'Vega10_r', 'Vega20', 'Vega20_r', 'Vega20b', 'Vega20b_r', 'Vega20c', 'Vega20c_r', 'Wistia', 'Wistia_r', 'YlGn', 'YlGnBu', 'YlGnBu_r', 'YlGn_r', 'YlOrBr', 'YlOrBr_r', 'YlOrRd', 'YlOrRd_r', 'afmhot', 'afmhot_r', 'autumn', 'autumn_r', 'binary', 'binary_r', 'bone', 'bone_r', 'brg', 'brg_r', 'bwr', 'bwr_r', 'cool', 'cool_r', 'coolwarm', 'coolwarm_r', 'copper', 'copper_r', 'cubehelix', 'cubehelix_r', 'flag', 'flag_r', 'gist_earth', 'gist_earth_r', 'gist_gray', 'gist_gray_r', 'gist_heat', 'gist_heat_r', 'gist_ncar', 'gist_ncar_r', 'gist_rainbow', 'gist_rainbow_r', 'gist_stern', 'gist_stern_r', 'gist_yarg', 'gist_yarg_r', 'gnuplot', 'gnuplot2', 'gnuplot2_r', 'gnuplot_r', 'gray', 'gray_r', 'hot', 'hot_r', 'hsv', 'hsv_r', 'icefire', 'icefire_r', 'inferno', 'inferno_r', 'jet', 'jet_r', 'magma', 'magma_r', 'mako', 'mako_r', 'nipy_spectral', 'nipy_spectral_r', 'ocean', 'ocean_r', 'pink', 'pink_r', 'plasma', 'plasma_r', 'prism', 'prism_r', 'rainbow', 'rainbow_r', 'rocket', 'rocket_r', 'seismic', 'seismic_r', 'spectral', 'spectral_r', 'spring', 'spring_r', 'summer', 'summer_r', 'tab10', 'tab10_r', 'tab20', 'tab20_r', 'tab20b', 'tab20b_r', 'tab20c', 'tab20c_r', 'terrain', 'terrain_r', 'viridis', 'viridis_r', 'vlag', 'vlag_r', 'winter', 'winter_r'}), optional
+ − 341 The matplotlib colorscheme to generate the heatmap with.
+ − 342
+ − 343 Returns
+ − 344 -------
+ − 345 visualization : Visualization
+ − 346 \
+ − 347 ]]>
+ − 348 </help>
+ − 349 </tool>
