Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/qiime_gneiss_dendrogram-heatmap.xml @ 0:370e0b6e9826 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children de4c22a52df4
comparison
equal deleted inserted replaced
-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2019.4">
3 <description> - Dendrogram heatmap.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime gneiss dendrogram-heatmap
9
10 --i-table=$itable
11 --i-tree=$itree
12 --m-metadata-column="$mmetadatacolumn"
13
14
15 #if $input_files_mmetadatafile:
16 #def list_dict_to_string(list_dict):
17 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
18 #for d in list_dict[1:]:
19 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
20 #end for
21 #return $file_list
22 #end def
23 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
24 #end if
25
26
27 #if $ppseudocount:
28 --p-pseudocount=$ppseudocount
29 #end if
30
31 #if $pndim:
32 --p-ndim=$pndim
33 #end if
34
35 #if str($pmethod) != 'None':
36 --p-method=$pmethod
37 #end if
38
39 #if str($pcolormap) != 'None':
40 --p-color-map=$pcolormap
41 #end if
42
43 --o-visualization=ovisualization
44 ;
45 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
46 && cp -r out/* '$ovisualization.files_path'
47 && mv '$ovisualization.files_path/index.html' '$ovisualization'
48 ]]></command>
49 <inputs>
50 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table that will be plotted as a heatmap. This table is assumed to have strictly positive values. [required]" name="itable" optional="False" type="data"/>
51 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT A hierarchy of feature identifiers where each Hierarchy tipcorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="itree" optional="False" type="data"/>
52 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to group the samples. [required]" name="mmetadatacolumn" optional="False" type="text"/>
53 <param label="--p-pseudocount: NUMBER The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5"/>
54 <param label="--p-ndim: INTEGER Number of dimensions to highlight. [default: 10]" name="pndim" optional="True" type="integer" value="10"/>
55 <param label="--p-method: " name="pmethod" optional="True" type="select">
56 <option selected="True" value="None">Selection is Optional</option>
57 <option value="clr">clr</option>
58 <option value="log">log</option>
59 </param>
60 <param label="--p-color-map: " name="pcolormap" optional="True" type="select">
61 <option selected="True" value="None">Selection is Optional</option>
62 <option value="viridis">viridis</option>
63 <option value="inferno">inferno</option>
64 <option value="plasma">plasma</option>
65 <option value="magma">magma</option>
66 <option value="Blues">Blues</option>
67 <option value="BuGn">BuGn</option>
68 <option value="BuPu">BuPu</option>
69 <option value="GnBu">GnBu</option>
70 <option value="Greens">Greens</option>
71 <option value="Greys">Greys</option>
72 <option value="Oranges">Oranges</option>
73 <option value="OrRd">OrRd</option>
74 <option value="PuBu">PuBu</option>
75 <option value="PuBuGn">PuBuGn</option>
76 <option value="PuRd">PuRd</option>
77 <option value="Purples">Purples</option>
78 <option value="RdPu">RdPu</option>
79 <option value="Reds">Reds</option>
80 <option value="YlGn">YlGn</option>
81 <option value="YlGnBu">YlGnBu</option>
82 <option value="YlOrBr">YlOrBr</option>
83 <option value="YlOrRd">YlOrRd</option>
84 <option value="afmhot">afmhot</option>
85 <option value="autumn">autumn</option>
86 <option value="bone">bone</option>
87 <option value="cool">cool</option>
88 <option value="copper">copper</option>
89 <option value="gist_heat">gist_heat</option>
90 <option value="gray">gray</option>
91 <option value="hot">hot</option>
92 <option value="pink">pink</option>
93 <option value="spring">spring</option>
94 <option value="summer">summer</option>
95 <option value="winter">winter</option>
96 <option value="BrBG">BrBG</option>
97 <option value="bwr">bwr</option>
98 <option value="coolwarm">coolwarm</option>
99 <option value="PiYG">PiYG</option>
100 <option value="PRGn">PRGn</option>
101 <option value="PuOr">PuOr</option>
102 <option value="RdBu">RdBu</option>
103 <option value="RdGy">RdGy</option>
104 <option value="RdYlBu">RdYlBu</option>
105 <option value="RdYlGn">RdYlGn</option>
106 <option value="Spectral">Spectral</option>
107 <option value="seismic">seismic</option>
108 <option value="Accent">Accent</option>
109 <option value="Dark2">Dark2</option>
110 <option value="Paired">Paired</option>
111 <option value="Pastel1">Pastel1</option>
112 <option value="Pastel2">Pastel2</option>
113 <option value="Set1">Set1</option>
114 <option value="Set2">Set2</option>
115 <option value="Set3">Set3</option>
116 <option value="Vega10">Vega10</option>
117 <option value="Vega20">Vega20</option>
118 <option value="Vega20b">Vega20b</option>
119 <option value="Vega20c">Vega20c</option>
120 <option value="gist_earth">gist_earth</option>
121 <option value="terrain">terrain</option>
122 <option value="ocean">ocean</option>
123 <option value="gist_stern">gist_stern</option>
124 <option value="brg">brg</option>
125 <option value="CMRmap">CMRmap</option>
126 <option value="cubehelix">cubehelix</option>
127 <option value="gnuplot">gnuplot</option>
128 <option value="gnuplot2">gnuplot2</option>
129 <option value="gist_ncar">gist_ncar</option>
130 <option value="nipy_spectral">nipy_spectral</option>
131 <option value="jet">jet</option>
132 <option value="rainbow">rainbow</option>
133 <option value="gist_rainbow">gist_rainbow</option>
134 <option value="hsv">hsv</option>
135 <option value="flag">flag</option>
136 <option value="prism">prism</option>
137 </param>
138
139 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
140 <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" />
141 </repeat>
142
143 </inputs>
144 <outputs>
145 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
146 </outputs>
147 <help><![CDATA[
148 Dendrogram heatmap.
149 ###################
150
151 Visualize the feature table as a heatmap, with samples sorted along a
152 specified categorical metadata column and features clustered together
153 specified by the tree.
154
155 Parameters
156 ----------
157 table : FeatureTable[Frequency]
158 The feature table that will be plotted as a heatmap. This table is
159 assumed to have strictly positive values.
160 tree : Hierarchy
161 A hierarchy of feature identifiers where each tipcorresponds to the
162 feature identifiers in the table. This tree can contain tip ids that
163 are not present in the table, but all feature ids in the table must be
164 present in this tree.
165 metadata : MetadataColumn[Categorical]
166 Categorical metadata column to group the samples.
167 pseudocount : Float, optional
168 The pseudocount to add to avoid division by zero.
169 ndim : Int, optional
170 Number of dimensions to highlight.
171 method : Str % Choices('clr', 'log'), optional
172 Specifies how the data should be normalized for display.Options include
173 'log' or 'clr' (default='clr').
174 color_map : Str % Choices('viridis', 'inferno', 'plasma', 'magma', 'Blues', 'BuGn', 'BuPu', 'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd', 'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu', 'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'cool', 'copper', 'gist_heat', 'gray', 'hot', 'pink', 'spring', 'summer', 'winter', 'BrBG', 'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral', 'seismic', 'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'gist_earth', 'terrain', 'ocean', 'gist_stern', 'brg', 'CMRmap', 'cubehelix', 'gnuplot', 'gnuplot2', 'gist_ncar', 'nipy_spectral', 'jet', 'rainbow', 'gist_rainbow', 'hsv', 'flag', 'prism'), optional
175 Specifies the color map for plotting the heatmap. See
176 https://matplotlib.org/examples/color/colormaps_reference.html for more
177 details.
178
179 Returns
180 -------
181 visualization : Visualization
182 ]]></help>
183 <macros>
184 <import>qiime_citation.xml</import>
185 </macros>
186 <expand macro="qiime_citation"/>
187 </tool>