Mercurial > repos > malex > secimtools

comparison scatter_plot_3D.xml @ 1:2e7d47c0b027 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author malex
date Mon, 08 Mar 2021 22:04:06 +0000
parents
children
comparison
equal deleted inserted replaced
0:b54326490b4d 1:2e7d47c0b027
1 <tool id="secimtools_scatter_plot_3D" name="Scatter Plot 3D" version="@WRAPPER_VERSION@">
2 <description>- A standalone tool.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 scatter_plot_3D.py
9 --input $input
10 --ID $uniqID
11
12 --X $x
13 --Y $y
14 --Z $z
15 --figure $figure
16
17 #if $design
18 --design $design
19 #end if
20
21 #if $group
22 --group $group
23 #end if
24
25 #if $color
26 --color $color
27 #end if
28
29 #if $palette
30 --palette $palette
31 #end if
32
33 #if $rotation
34 --rotation $rotation
35 #end if
36
37 #if $elevation
38 --elevation $elevation
39 #end if
40 ]]></command>
41 <inputs>
42 <param name="input" type="data" format="tabular" label="Long Dataset" help="Input dataset in tab-separated long format. Please see the description of the file format below. If the file is not tab separated see TIP below."/>
43 <param name="uniqID" type="text" size="30" value="" label="SampleID" help="Name of the column in your long dataset with unique sample identifiers (sampleID). If coloring by group, sampleIDs must match sampleIDs in the Design File."/>
44 <param name="x" type="text" size="30" value="" label="X Group Title" help="Name of the column in long format dataset for X values."/>
45 <param name="y" type="text" size="30" value="" label="Y Group Title" help="Name of the column in long format dataset for Y values."/>
46 <param name="z" type="text" size="30" value="" label="Z Group Title" help="Name of the column in long format dataset for Z values."/>
47 <param name="rotation" type="text" size="30" value="" label="Azimuth (Rotation) Angle for Viewing [Optional]" help="The azimuth (rotation) angle for viewing in degrees. Default = 45 degrees. The ideal azimuth (rotation) angle may be a process of trial and error."/>
48 <param name="elevation" type="text" size="30" value="" label="Elevation Angle for Viewing [Optional]" help="The elevation angle for viewing in degrees. Default = 45 degrees. The ideal elevation angle may be a process of trial and error."/>
49 <param name="design" type="data" format="tabular" optional="true" label="Design File [Optional]" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
50 <param name="group" type="text" size="30" value="" label="Group/Treatment [Optional]" help="Name of the column in your Design File that contains group classification that will be used for coloring."/>
51 <param name="palette" type="text" size="30" label="Palette [Optional]" help="Select color palette. Default = tableau. Other options include diverging, qualitative, sequential, cubehelix, and wesanderson. Please see the descriptions for the palettes below."/>
52 <param name="color" type="text" size="30" label="Color Scheme [Optional]" help="Select color scheme within the palette. The default color scheme for palette tableau = Tableau_20. User must specify Color Scheme if the Palette field has been filled. Please see the descriptions for the color schemes below."/>
53 </inputs>
54 <outputs>
55 <data format="pdf" name="figure" label="${tool.name} on ${on_string}: scatter plots"/>
56 </outputs>
57 <tests>
58 <test>
59 <param name="input" value="ST000006_principal_component_analysis_score_out.tsv"/>
60 <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
61 <param name="uniqID" value="sampleID" />
62 <param name="group" value="White_wine_type_and_source" />
63 <param name="x" value="PC1" />
64 <param name="y" value="PC2" />
65 <param name="z" value="PC3" />
66 <output name="figure" file="ST000006_scatter_plot_3D_default_figure.pdf" compare="sim_size" delta="10000" />
67 </test>
68 <test>
69 <param name="input" value="ST000006_principal_component_analysis_score_out.tsv"/>
70 <param name="design" value="ST000006_design_group_name_underscore.tsv"/>
71 <param name="uniqID" value="sampleID" />
72 <param name="group" value="White_wine_type_and_source" />
73 <param name="x" value="PC1" />
74 <param name="y" value="PC2" />
75 <param name="z" value="PC3" />
76 <param name="rotation" value="30" />
77 <param name="elevation" value="23" />
78 <param name="palette" value="sequential" />
79 <param name="color" value="Blues_3" />
80 <output name="figure" file="ST000006_scatter_plot_3D_palette_color_figure.pdf" compare="sim_size" delta="10000" />
81 </test>
82 </tests>
83 <help><![CDATA[
84
85 @TIP_AND_WARNING@
86
87
88 **Tool Description**
89
90 The tool provides a 3D scatter plot of values in a Long Format file. Please see the description of the Long Format below.
91 If coloring by group is desired, the column with the sample names in the Long Format dataset has to have the name "sampleID" to match the name in the Design File.
92 Scatter plot 2D allows the user to plot any pair of values from the Principal Component Analysis (PCA) output or plot other data.
93
94 NOTE: The user should ensure that the input datasets have no missing values.
95
96 The user has an option to specify the palette and the color scheme within the palette.
97 If the palette is specified by the user, the color scheme must to be specified.
98 The list of available palettes are:
99
100 diverging,
101 qualitative,
102 sequential,
103 cubehelix,
104 tableau (default), and
105 wesanderson.
106
107 The lists of corresponding color schemes for each palattes are available via the links below:
108
109 https://jiffyclub.github.io/palettable/tableau/
110
111 https://jiffyclub.github.io/palettable/colorbrewer/diverging/
112
113 https://jiffyclub.github.io/palettable/colorbrewer/qualitative/
114
115 https://jiffyclub.github.io/palettable/colorbrewer/sequential/
116
117 https://jiffyclub.github.io/palettable/cubehelix/
118
119 https://jiffyclub.github.io/palettable/wesanderson/
120
121
122 **NOTE:** The user should ensure that the Long Format and Design File datasets have no missing values.
123
124
125 --------------------------------------------------------------------------------
126
127 **Input**
128
129 - Two input datasets are required.
130
131 @LONG@
132
133
134 **Sample ID**
135
136 - Name of the column in your Long Dataset that has the unique sample IDs. If coloring by group is desired based on the Design File sample IDs have to be saved in a column with the name sampleID to match the name in the Design File
137
138
139 **X Group Title**
140
141 - Name of the column in the Long Format dataset for X values.
142
143 **Y Group Title**
144
145 - Name of the column in the Long Format dataset for Y values.
146
147 **Z Group Title**
148
149 - Name of the column in the Long Format dataset for Z values.
150
151 **Azimuth (Rotation) Angle for Viewing [Optional]:**
152
153 - The azimuth (rotation) angle for viewing in degrees. The default value = 45 degrees. The ideal azimuth (rotation) angle for viewing may involve trial and error.
154
155 **Elevation Angle for Viewing [Optional]:**
156
157 - The elevation angle for viewing in degrees. The default value = 45 degrees. The ideal elevation angle for viewing may involve trial and error.
158
159 @DF@
160
161 **Group/Treatment [Optional]**
162
163 - Name of the column in your Design File that contains group classification for coloring.
164
165 **Palette [Optional]**
166
167 - Choice of the palette. Default = tableau. The other options include: diverging, qualitative, sequential, cubehelix, tableau, and wesanderson.
168
169 **Color Scheme [Optional]**
170
171 - Choice of the color scheme within the palette. The default color scheme for palette tableau is Tableau_20. User has to specify Color Scheme if the Palette field has been filled.
172
173 --------------------------------------------------------------------------------
174
175 **Output**
176
177 The tool produces a PDF file containing a 3D scatter plot.
178 The coloring of the features by group and the corresponding legend will be included in the plot if the user provides the Design File and Palette.
179
180 ]]></help>
181 <expand macro="citations"/>
182 </tool>