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comparison qiime2/qiime_feature-table_heatmap.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap" version="2019.7"> 2 <tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap"
3 <description> - Generate a heatmap representation of a feature table</description> 3 version="2020.8">
4 <requirements> 4 <description>Generate a heatmap representation of a feature table</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 qiime feature-table heatmap 8 <command><![CDATA[
9 qiime feature-table heatmap
9 10
10 --i-table=$itable 11 --i-table=$itable
11 12 # if $input_files_msamplemetadatafile:
12 13 # def list_dict_to_string(list_dict):
13 --m-metadata-file=$mmedatafile 14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
14 15 # for d in list_dict[1:]:
15 16 # set $file_list = $file_list + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
16 #if str($mmetadatacolumn): 17 # end for
17 --m-metadata-column="$mmetadatacolumn" 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
18 #end if 81 #end if
19 82
20 #if $pnonormalize: 83 #if $pnonormalize:
21 --p-no-normalize 84 --p-no-normalize
22 #end if 85 #end if
23 86
24 #if str($ptitle): 87 #if str($ptitle):
25 --p-title="$ptitle" 88 --p-title=$ptitle
26 #end if 89 #end if
27
28 #if str($pmetric) != 'None': 90 #if str($pmetric) != 'None':
29 --p-metric=$pmetric 91 --p-metric=$pmetric
30 #end if 92 #end if
31 93
32 #if str($pmethod) != 'None': 94 #if str($pmethod) != 'None':
33 --p-method=$pmethod 95 --p-method=$pmethod
34 #end if 96 #end if
35 97
36 #if str($pcluster) != 'None': 98 #if str($pcluster) != 'None':
37 --p-cluster=$pcluster 99 --p-cluster=$pcluster
38 #end if 100 #end if
39 101
40 #if str($pcolorscheme) != 'None': 102 #if str($pcolorscheme) != 'None':
41 --p-color-scheme=$pcolorscheme 103 --p-color-scheme=$pcolorscheme
42 #end if 104 #end if
43 105
44 --o-visualization=ovisualization 106 --o-visualization=ovisualization
107
108 #if str($examples) != 'None':
109 --examples=$examples
110 #end if
111
45 ; 112 ;
46 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' 113 cp ogroupedtable.qza $ogroupedtable
114
115 ;
116 qiime tools export ovisualization.qzv --output-path out
117 && mkdir -p '$ovisualization.files_path'
47 && cp -r out/* '$ovisualization.files_path' 118 && cp -r out/* '$ovisualization.files_path'
48 && mv '$ovisualization.files_path/index.html' '$ovisualization' 119 && mv '$ovisualization.files_path/index.html' '$ovisualization'
49 ]]></command> 120
50 <inputs> 121 ]]></command>
51 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to visualize. [required]" name="itable" optional="False" type="data"/> 122 <inputs>
52 <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"/> 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" />
53 <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"/> 124 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
54 <param label="--p-title: TEXT Optional custom plot title. [optional]" name="ptitle" optional="True" type="text"/> 125 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
55 <param label="--p-metric: " name="pmetric" optional="True" type="select"> 126 </repeat>
56 <option selected="True" value="None">Selection is Optional</option> 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" />
57 <option value="kulsinski">kulsinski</option> 128 <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
58 <option value="correlation">correlation</option> 129 <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
59 <option value="hamming">hamming</option> 130 </repeat>
60 <option value="canberra">canberra</option> 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" />
61 <option value="sqeuclidean">sqeuclidean</option> 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" />
62 <option value="sokalmichener">sokalmichener</option> 133 <param label="--p-title: TEXT Optional custom plot title. [optional]" name="ptitle" optional="False" type="text" />
63 <option value="cityblock">cityblock</option> 134 <param label="--p-metric: " name="pmetric" optional="True" type="select">
64 <option value="braycurtis">braycurtis</option> 135 <option selected="True" value="None">Selection is Optional</option>
65 <option value="matching">matching</option> 136 <option value="euclidean">euclidean</option>
66 <option value="russellrao">russellrao</option> 137 <option value="cityblock">cityblock</option>
67 <option value="cosine">cosine</option> 138 <option value="matching">matching</option>
68 <option value="yule">yule</option> 139 <option value="russellrao">russellrao</option>
69 <option value="minkowski">minkowski</option> 140 <option value="sokalmichener">sokalmichener</option>
70 <option value="euclidean">euclidean</option> 141 <option value="kulsinski">kulsinski</option>
71 <option value="rogerstanimoto">rogerstanimoto</option> 142 <option value="chebyshev">chebyshev</option>
72 <option value="seuclidean">seuclidean</option> 143 <option value="hamming">hamming</option>
73 <option value="jaccard">jaccard</option> 144 <option value="dice">dice</option>
74 <option value="sokalsneath">sokalsneath</option> 145 <option value="yule">yule</option>
75 <option value="chebyshev">chebyshev</option> 146 <option value="rogerstanimoto">rogerstanimoto</option>
76 <option value="dice">dice</option> 147 <option value="braycurtis">braycurtis</option>
77 <option value="mahalanobis">mahalanobis</option> 148 <option value="cosine">cosine</option>
78 </param> 149 <option value="minkowski">minkowski</option>
79 <param label="--p-method: " name="pmethod" optional="True" type="select"> 150 <option value="correlation">correlation</option>
80 <option selected="True" value="None">Selection is Optional</option> 151 <option value="sokalsneath">sokalsneath</option>
81 <option value="complete">complete</option> 152 <option value="seuclidean">seuclidean</option>
82 <option value="centroid">centroid</option> 153 <option value="canberra">canberra</option>
83 <option value="weighted">weighted</option> 154 <option value="mahalanobis">mahalanobis</option>
84 <option value="single">single</option> 155 <option value="jaccard">jaccard</option>
85 <option value="ward">ward</option> 156 <option value="sqeuclidean">sqeuclidean</option>
86 <option value="average">average</option> 157 </param>
87 <option value="median">median</option> 158 <param label="--p-method: " name="pmethod" optional="True" type="select">
88 </param> 159 <option selected="True" value="None">Selection is Optional</option>
89 <param label="--p-cluster: " name="pcluster" optional="True" type="select"> 160 <option value="centroid">centroid</option>
90 <option selected="True" value="None">Selection is Optional</option> 161 <option value="median">median</option>
91 <option value="features">features</option> 162 <option value="weighted">weighted</option>
92 <option value="both">both</option> 163 <option value="average">average</option>
93 <option value="samples">samples</option> 164 <option value="single">single</option>
94 <option value="none">none</option> 165 <option value="complete">complete</option>
95 </param> 166 <option value="ward">ward</option>
96 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select"> 167 </param>
97 <option selected="True" value="None">Selection is Optional</option> 168 <param label="--p-cluster: " name="pcluster" optional="True" type="select">
98 <option value="bone">bone</option> 169 <option selected="True" value="None">Selection is Optional</option>
99 <option value="PRGn_r">PRGn_r</option> 170 <option value="both">both</option>
100 <option value="Vega10_r">Vega10_r</option> 171 <option value="none">none</option>
101 <option value="GnBu">GnBu</option> 172 <option value="features">features</option>
102 <option value="hsv">hsv</option> 173 <option value="samples">samples</option>
103 <option value="binary_r">binary_r</option> 174 </param>
104 <option value="GnBu_r">GnBu_r</option> 175 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
105 <option value="icefire">icefire</option> 176 <option selected="True" value="None">Selection is Optional</option>
106 <option value="winter">winter</option> 177 <option value="Spectral">Spectral</option>
107 <option value="BuGn_r">BuGn_r</option> 178 <option value="flag">flag</option>
108 <option value="plasma_r">plasma_r</option> 179 <option value="jet">jet</option>
109 <option value="Vega20_r">Vega20_r</option> 180 <option value="Vega20">Vega20</option>
110 <option value="summer_r">summer_r</option> 181 <option value="terrain">terrain</option>
111 <option value="cool_r">cool_r</option> 182 <option value="jet_r">jet_r</option>
112 <option value="Spectral">Spectral</option> 183 <option value="Vega20c_r">Vega20c_r</option>
113 <option value="gist_heat_r">gist_heat_r</option> 184 <option value="Oranges_r">Oranges_r</option>
114 <option value="Vega20b_r">Vega20b_r</option> 185 <option value="spectral">spectral</option>
115 <option value="mako_r">mako_r</option> 186 <option value="summer">summer</option>
116 <option value="RdBu_r">RdBu_r</option> 187 <option value="BuPu_r">BuPu_r</option>
117 <option value="cubehelix">cubehelix</option> 188 <option value="tab20b_r">tab20b_r</option>
118 <option value="tab20b_r">tab20b_r</option> 189 <option value="Pastel1">Pastel1</option>
119 <option value="CMRmap">CMRmap</option> 190 <option value="gnuplot_r">gnuplot_r</option>
120 <option value="Greys">Greys</option> 191 <option value="seismic">seismic</option>
121 <option value="PuOr">PuOr</option> 192 <option value="icefire">icefire</option>
122 <option value="cubehelix_r">cubehelix_r</option> 193 <option value="Set1">Set1</option>
123 <option value="Wistia">Wistia</option> 194 <option value="bwr">bwr</option>
124 <option value="gnuplot2">gnuplot2</option> 195 <option value="coolwarm_r">coolwarm_r</option>
125 <option value="bwr">bwr</option> 196 <option value="ocean_r">ocean_r</option>
126 <option value="gnuplot_r">gnuplot_r</option> 197 <option value="gist_gray_r">gist_gray_r</option>
127 <option value="viridis">viridis</option> 198 <option value="autumn">autumn</option>
128 <option value="gist_ncar_r">gist_ncar_r</option> 199 <option value="BrBG">BrBG</option>
129 <option value="gist_ncar">gist_ncar</option> 200 <option value="Pastel2">Pastel2</option>
130 <option value="plasma">plasma</option> 201 <option value="GnBu">GnBu</option>
131 <option value="PuRd">PuRd</option> 202 <option value="Vega20b_r">Vega20b_r</option>
132 <option value="afmhot">afmhot</option> 203 <option value="tab20c">tab20c</option>
133 <option value="icefire_r">icefire_r</option> 204 <option value="Paired">Paired</option>
134 <option value="tab20b">tab20b</option> 205 <option value="YlOrRd_r">YlOrRd_r</option>
135 <option value="gist_yarg_r">gist_yarg_r</option> 206 <option value="icefire_r">icefire_r</option>
136 <option value="hot">hot</option> 207 <option value="cubehelix_r">cubehelix_r</option>
137 <option value="YlOrRd_r">YlOrRd_r</option> 208 <option value="CMRmap_r">CMRmap_r</option>
138 <option value="Vega20c">Vega20c</option> 209 <option value="RdBu">RdBu</option>
139 <option value="Dark2_r">Dark2_r</option> 210 <option value="YlGn_r">YlGn_r</option>
140 <option value="Set3">Set3</option> 211 <option value="gray_r">gray_r</option>
141 <option value="PuBu">PuBu</option> 212 <option value="mako_r">mako_r</option>
142 <option value="magma">magma</option> 213 <option value="OrRd_r">OrRd_r</option>
143 <option value="Pastel2">Pastel2</option> 214 <option value="Vega10">Vega10</option>
144 <option value="terrain">terrain</option> 215 <option value="Set3">Set3</option>
145 <option value="autumn_r">autumn_r</option> 216 <option value="RdYlGn_r">RdYlGn_r</option>
146 <option value="spectral">spectral</option> 217 <option value="hsv">hsv</option>
147 <option value="brg">brg</option> 218 <option value="cool_r">cool_r</option>
148 <option value="Set3_r">Set3_r</option> 219 <option value="Spectral_r">Spectral_r</option>
149 <option value="coolwarm">coolwarm</option> 220 <option value="rainbow">rainbow</option>
150 <option value="Set2_r">Set2_r</option> 221 <option value="cividis">cividis</option>
151 <option value="Paired_r">Paired_r</option> 222 <option value="Blues_r">Blues_r</option>
152 <option value="tab20c_r">tab20c_r</option> 223 <option value="PuOr_r">PuOr_r</option>
153 <option value="mako">mako</option> 224 <option value="binary_r">binary_r</option>
154 <option value="gist_rainbow_r">gist_rainbow_r</option> 225 <option value="RdGy">RdGy</option>
155 <option value="RdBu">RdBu</option> 226 <option value="Pastel2_r">Pastel2_r</option>
156 <option value="PuBu_r">PuBu_r</option> 227 <option value="Pastel1_r">Pastel1_r</option>
157 <option value="jet_r">jet_r</option> 228 <option value="Dark2">Dark2</option>
158 <option value="gist_earth_r">gist_earth_r</option> 229 <option value="vlag">vlag</option>
159 <option value="Greys_r">Greys_r</option> 230 <option value="binary">binary</option>
160 <option value="gray">gray</option> 231 <option value="pink">pink</option>
161 <option value="winter_r">winter_r</option> 232 <option value="Purples">Purples</option>
162 <option value="rocket">rocket</option> 233 <option value="cividis_r">cividis_r</option>
163 <option value="Set2">Set2</option> 234 <option value="gray">gray</option>
164 <option value="seismic_r">seismic_r</option> 235 <option value="seismic_r">seismic_r</option>
165 <option value="Pastel1">Pastel1</option> 236 <option value="Greys">Greys</option>
166 <option value="RdYlGn_r">RdYlGn_r</option> 237 <option value="tab20">tab20</option>
167 <option value="copper">copper</option> 238 <option value="BuPu">BuPu</option>
168 <option value="spring_r">spring_r</option> 239 <option value="RdBu_r">RdBu_r</option>
169 <option value="BuGn">BuGn</option> 240 <option value="gnuplot2_r">gnuplot2_r</option>
170 <option value="Greens">Greens</option> 241 <option value="Accent_r">Accent_r</option>
171 <option value="Blues">Blues</option> 242 <option value="magma">magma</option>
172 <option value="PiYG_r">PiYG_r</option> 243 <option value="copper_r">copper_r</option>
173 <option value="YlGnBu">YlGnBu</option> 244 <option value="inferno">inferno</option>
174 <option value="Paired">Paired</option> 245 <option value="nipy_spectral_r">nipy_spectral_r</option>
175 <option value="YlGn_r">YlGn_r</option> 246 <option value="pink_r">pink_r</option>
176 <option value="RdPu_r">RdPu_r</option> 247 <option value="copper">copper</option>
177 <option value="BrBG_r">BrBG_r</option> 248 <option value="Dark2_r">Dark2_r</option>
178 <option value="bone_r">bone_r</option> 249 <option value="YlGnBu_r">YlGnBu_r</option>
179 <option value="RdYlBu">RdYlBu</option> 250 <option value="Wistia_r">Wistia_r</option>
180 <option value="gist_rainbow">gist_rainbow</option> 251 <option value="spectral_r">spectral_r</option>
181 <option value="bwr_r">bwr_r</option> 252 <option value="cubehelix">cubehelix</option>
182 <option value="inferno_r">inferno_r</option> 253 <option value="tab20_r">tab20_r</option>
183 <option value="inferno">inferno</option> 254 <option value="viridis">viridis</option>
184 <option value="gist_stern_r">gist_stern_r</option> 255 <option value="RdYlBu">RdYlBu</option>
185 <option value="gray_r">gray_r</option> 256 <option value="Blues">Blues</option>
186 <option value="Purples">Purples</option> 257 <option value="rocket_r">rocket_r</option>
187 <option value="RdGy">RdGy</option> 258 <option value="Set1_r">Set1_r</option>
188 <option value="hot_r">hot_r</option> 259 <option value="brg_r">brg_r</option>
189 <option value="YlOrBr_r">YlOrBr_r</option> 260 <option value="bone_r">bone_r</option>
190 <option value="nipy_spectral">nipy_spectral</option> 261 <option value="gist_ncar_r">gist_ncar_r</option>
191 <option value="nipy_spectral_r">nipy_spectral_r</option> 262 <option value="afmhot">afmhot</option>
192 <option value="ocean">ocean</option> 263 <option value="RdYlBu_r">RdYlBu_r</option>
193 <option value="Set1">Set1</option> 264 <option value="gist_earth_r">gist_earth_r</option>
194 <option value="Dark2">Dark2</option> 265 <option value="RdGy_r">RdGy_r</option>
195 <option value="Oranges">Oranges</option> 266 <option value="Vega10_r">Vega10_r</option>
196 <option value="Pastel1_r">Pastel1_r</option> 267 <option value="gist_rainbow_r">gist_rainbow_r</option>
197 <option value="Oranges_r">Oranges_r</option> 268 <option value="spring">spring</option>
198 <option value="Pastel2_r">Pastel2_r</option> 269 <option value="Set3_r">Set3_r</option>
199 <option value="YlGn">YlGn</option> 270 <option value="magma_r">magma_r</option>
200 <option value="Vega20b">Vega20b</option> 271 <option value="mako">mako</option>
201 <option value="PuRd_r">PuRd_r</option> 272 <option value="PuRd">PuRd</option>
202 <option value="PuBuGn_r">PuBuGn_r</option> 273 <option value="gnuplot2">gnuplot2</option>
203 <option value="afmhot_r">afmhot_r</option> 274 <option value="Paired_r">Paired_r</option>
204 <option value="spring">spring</option> 275 <option value="Vega20b">Vega20b</option>
205 <option value="tab20_r">tab20_r</option> 276 <option value="Accent">Accent</option>
206 <option value="PuBuGn">PuBuGn</option> 277 <option value="hsv_r">hsv_r</option>
207 <option value="gist_yarg">gist_yarg</option> 278 <option value="ocean">ocean</option>
208 <option value="PiYG">PiYG</option> 279 <option value="gist_earth">gist_earth</option>
209 <option value="flag">flag</option> 280 <option value="afmhot_r">afmhot_r</option>
210 <option value="rainbow_r">rainbow_r</option> 281 <option value="bone">bone</option>
211 <option value="hsv_r">hsv_r</option> 282 <option value="rocket">rocket</option>
212 <option value="prism_r">prism_r</option> 283 <option value="RdYlGn">RdYlGn</option>
213 <option value="ocean_r">ocean_r</option> 284 <option value="bwr_r">bwr_r</option>
214 <option value="magma_r">magma_r</option> 285 <option value="RdPu_r">RdPu_r</option>
215 <option value="flag_r">flag_r</option> 286 <option value="BuGn">BuGn</option>
216 <option value="Blues_r">Blues_r</option> 287 <option value="PuBu">PuBu</option>
217 <option value="gnuplot2_r">gnuplot2_r</option> 288 <option value="hot_r">hot_r</option>
218 <option value="gist_gray">gist_gray</option> 289 <option value="Vega20c">Vega20c</option>
219 <option value="spectral_r">spectral_r</option> 290 <option value="gist_yarg">gist_yarg</option>
220 <option value="CMRmap_r">CMRmap_r</option> 291 <option value="tab10">tab10</option>
221 <option value="rainbow">rainbow</option> 292 <option value="coolwarm">coolwarm</option>
222 <option value="gnuplot">gnuplot</option> 293 <option value="winter_r">winter_r</option>
223 <option value="vlag">vlag</option> 294 <option value="plasma_r">plasma_r</option>
224 <option value="Set1_r">Set1_r</option> 295 <option value="Wistia">Wistia</option>
225 <option value="Accent">Accent</option> 296 <option value="BuGn_r">BuGn_r</option>
226 <option value="coolwarm_r">coolwarm_r</option> 297 <option value="Set2">Set2</option>
227 <option value="brg_r">brg_r</option> 298 <option value="Vega20_r">Vega20_r</option>
228 <option value="pink_r">pink_r</option> 299 <option value="hot">hot</option>
229 <option value="YlOrBr">YlOrBr</option> 300 <option value="brg">brg</option>
230 <option value="Vega20c_r">Vega20c_r</option> 301 <option value="BrBG_r">BrBG_r</option>
231 <option value="Wistia_r">Wistia_r</option> 302 <option value="gist_heat">gist_heat</option>
232 <option value="RdGy_r">RdGy_r</option> 303 <option value="YlOrRd">YlOrRd</option>
233 <option value="tab20">tab20</option> 304 <option value="inferno_r">inferno_r</option>
234 <option value="BrBG">BrBG</option> 305 <option value="viridis_r">viridis_r</option>
235 <option value="rocket_r">rocket_r</option> 306 <option value="gist_stern_r">gist_stern_r</option>
236 <option value="OrRd_r">OrRd_r</option> 307 <option value="tab20c_r">tab20c_r</option>
237 <option value="YlGnBu_r">YlGnBu_r</option> 308 <option value="gist_gray">gist_gray</option>
238 <option value="viridis_r">viridis_r</option> 309 <option value="Reds_r">Reds_r</option>
239 <option value="copper_r">copper_r</option> 310 <option value="flag_r">flag_r</option>
240 <option value="gist_heat">gist_heat</option> 311 <option value="Purples_r">Purples_r</option>
241 <option value="Vega10">Vega10</option> 312 <option value="vlag_r">vlag_r</option>
242 <option value="PuOr_r">PuOr_r</option> 313 <option value="summer_r">summer_r</option>
243 <option value="binary">binary</option> 314 <option value="Greys_r">Greys_r</option>
244 <option value="pink">pink</option> 315 <option value="PRGn">PRGn</option>
245 <option value="Reds">Reds</option> 316 <option value="PiYG">PiYG</option>
246 <option value="Purples_r">Purples_r</option> 317 <option value="gist_ncar">gist_ncar</option>
247 <option value="cool">cool</option> 318 <option value="Oranges">Oranges</option>
248 <option value="prism">prism</option> 319 <option value="Reds">Reds</option>
249 <option value="terrain_r">terrain_r</option> 320 <option value="GnBu_r">GnBu_r</option>
250 <option value="BuPu_r">BuPu_r</option> 321 <option value="RdPu">RdPu</option>
251 <option value="Spectral_r">Spectral_r</option> 322 <option value="YlOrBr_r">YlOrBr_r</option>
252 <option value="Greens_r">Greens_r</option> 323 <option value="autumn_r">autumn_r</option>
253 <option value="gist_gray_r">gist_gray_r</option> 324 <option value="YlGn">YlGn</option>
254 <option value="RdYlGn">RdYlGn</option> 325 <option value="CMRmap">CMRmap</option>
255 <option value="tab20c">tab20c</option> 326 <option value="gnuplot">gnuplot</option>
256 <option value="Reds_r">Reds_r</option> 327 <option value="rainbow_r">rainbow_r</option>
257 <option value="tab10">tab10</option> 328 <option value="PiYG_r">PiYG_r</option>
258 <option value="summer">summer</option> 329 <option value="Greens">Greens</option>
259 <option value="gist_stern">gist_stern</option> 330 <option value="YlOrBr">YlOrBr</option>
260 <option value="tab10_r">tab10_r</option> 331 <option value="prism_r">prism_r</option>
261 <option value="YlOrRd">YlOrRd</option> 332 <option value="winter">winter</option>
262 <option value="jet">jet</option> 333 <option value="gist_yarg_r">gist_yarg_r</option>
263 <option value="Vega20">Vega20</option> 334 <option value="Set2_r">Set2_r</option>
264 <option value="vlag_r">vlag_r</option> 335 <option value="nipy_spectral">nipy_spectral</option>
265 <option value="RdPu">RdPu</option> 336 <option value="plasma">plasma</option>
266 <option value="OrRd">OrRd</option> 337 <option value="OrRd">OrRd</option>
267 <option value="Accent_r">Accent_r</option> 338 <option value="Greens_r">Greens_r</option>
268 <option value="autumn">autumn</option> 339 <option value="tab10_r">tab10_r</option>
269 <option value="BuPu">BuPu</option> 340 <option value="YlGnBu">YlGnBu</option>
270 <option value="RdYlBu_r">RdYlBu_r</option> 341 <option value="prism">prism</option>
271 <option value="gist_earth">gist_earth</option> 342 <option value="PRGn_r">PRGn_r</option>
272 <option value="seismic">seismic</option> 343 <option value="gist_heat_r">gist_heat_r</option>
273 <option value="PRGn">PRGn</option> 344 <option value="terrain_r">terrain_r</option>
274 </param> 345 <option value="tab20b">tab20b</option>
275 346 <option value="PuBuGn">PuBuGn</option>
276 <param label="--m-metadata-file" name="mmedatafile" optional="True" type="data" format="tabular,qza,no_unzip.zip" /> 347 <option value="PuBu_r">PuBu_r</option>
277 348 <option value="spring_r">spring_r</option>
278 </inputs> 349 <option value="gist_rainbow">gist_rainbow</option>
279 <outputs> 350 <option value="cool">cool</option>
280 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> 351 <option value="PuOr">PuOr</option>
281 </outputs> 352 <option value="PuRd_r">PuRd_r</option>
282 <help><![CDATA[ 353 <option value="gist_stern">gist_stern</option>
354 <option value="PuBuGn_r">PuBuGn_r</option>
355 </param>
356 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
357
358 </inputs>
359
360 <outputs>
361 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
362
363 </outputs>
364
365 <help><![CDATA[
283 Generate a heatmap representation of a feature table 366 Generate a heatmap representation of a feature table
284 #################################################### 367 ###############################################################
285 368
286 Generate a heatmap representation of a feature table with optional 369 Generate a heatmap representation of a feature table with optional
287 clustering on both the sample and feature axes. Tip: To generate a heatmap 370 clustering on both the sample and feature axes. Tip: To generate a heatmap
288 containing taxonomic annotations, use `qiime taxa collapse` to collapse the 371 containing taxonomic annotations, use `qiime taxa collapse` to collapse the
289 feature table at the desired taxonomic level. 372 feature table at the desired taxonomic level.
290 373
291 Parameters 374 Parameters
292 ---------- 375 ----------
293 table : FeatureTable[Frequency] 376 table : FeatureTable[Frequency]
294 The feature table to visualize. 377 The feature table to visualize.
295 metadata : MetadataColumn[Categorical], optional 378 sample_metadata : MetadataColumn[Categorical], optional
296 Annotate the sample IDs with these metadata values. When metadata is 379 Annotate the sample IDs with these sample metadata values. When
297 present and \`cluster\`='feature', samples will be sorted by the metadata 380 metadata is present and `cluster`='feature', samples will be sorted by
298 values. 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.
299 normalize : Bool, optional 386 normalize : Bool, optional
300 Normalize the feature table by adding a psuedocount of 1 and then 387 Normalize the feature table by adding a psuedocount of 1 and then
301 taking the log10 of the table. 388 taking the log10 of the table.
302 title : Str, optional 389 title : Str, optional
303 Optional custom plot title. 390 Optional custom plot title.
304 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 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
305 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea 392 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
306 born.clustermap.html#seaborn.clustermap for more detail). 393 born.clustermap.html#seaborn.clustermap for more detail).
307 method : Str % Choices('average', 'complete', 'median', 'centroid', 'single', 'ward', 'weighted'), optional 394 method : Str % Choices('complete', 'average', 'ward', 'median', 'weighted', 'centroid', 'single'), optional
308 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge 395 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
309 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail). 396 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
310 cluster : Str % Choices('features', 'samples', 'none', 'both'), optional 397 cluster : Str % Choices('both', 'features', 'none', 'samples'), optional
311 Specify which axes to cluster. 398 Specify which axes to cluster.
312 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 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
313 The matplotlib colorscheme to generate the heatmap with. 400 The matplotlib colorscheme to generate the heatmap with.
314 401
315 Returns 402 Returns
316 ------- 403 -------
317 visualization : Visualization 404 visualization : Visualization
318 ]]></help> 405 ]]></help>
319 <macros> 406 <macros>
320 <import>qiime_citation.xml</import> 407 <import>qiime_citation.xml</import>
321 </macros> 408 </macros>
322 <expand macro="qiime_citation"/> 409 <expand macro="qiime_citation"/>
323 </tool> 410 </tool>