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comparison macros.xml @ 0:a597d59df9ee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
author iuc
date Tue, 22 Aug 2017 06:42:56 -0400
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children 43778344b955
comparison
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-1:000000000000 0:a597d59df9ee
1 <?xml version="1.0"?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="@VERSION@">r-ggplot2</requirement>
6 <yield />
7 </requirements>
8 </xml>
9 <token name="@VERSION@">2.2.1</token>
10
11 <token name="@R_INIT@"><![CDATA[
12 ## Setup R error handling to go to stderr
13 options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
14
15 ## Unify locale settings
16 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
17 ]]></token>
18
19 <token name="@TRANSFORM@"><![CDATA[
20 #if $transform == "log2"
21 input["value"] <- log2(input["value"])
22 #elif $transform == "log2plus1"
23 input["value"] <- log2(input["value"]+1)
24 #elif $transform == "log10"
25 input["value"] <- log10(input["value"])
26 #elif $transform == "log10plus1"
27 input["value"] <- log10(input["value"]+1)
28 #end if
29 ]]></token>
30
31 <xml name="transform">
32 <param name="transform" type="select" label="Advanced - log transformation">
33 <option value="none">Plot the data as it is</option>
34 <option value="log2">Log2(value) transform my data</option>
35 <option value="log2plus1">Log2(value+1) transform my data</option>
36 <option value="log10">Log10(value) transform my data</option>
37 <option value="log10plus1">Log10(value+1) transform my data</option>
38 </param>
39 </xml>
40
41 <token name="@XY_SCALING@"><![CDATA[
42 #Choose between automatically scaled x and y axis or user defined
43 #if $scaling.plot_scaling == "Automatic"
44 gg_scalex = NULL
45 gg_scaley = NULL
46 #else
47 gg_scalex = xlim($scaling.xaxismin, $scaling.xaxismax)
48 gg_scaley = ylim($scaling.yaxismin, $scaling.yaxismax)
49 #end if
50 ]]></token>
51
52 <xml name="xy_scaling">
53 <conditional name="scaling">
54 <param name="plot_scaling" type="select" label="Advanced - Axis scaling">
55 <option value="Automatic" selected="True">Automatic axis scaling</option>
56 <option value="Defined">User deined axis scales</option>
57 </param>
58 <when value="Automatic">
59 <!--Do nothing here -->
60 </when>
61 <when value="Defined">
62 <param name="xaxismin" type="integer" value="0" label="minimal range of x-axis" />
63 <param name="xaxismax" type="integer" value="3" label="maximal range of x-axis" />
64 <param name="yaxismin" type="integer" value="0" label="minimal range of y-axis" />
65 <param name="yaxismax" type="integer" value="3" label="maximal range of y-axis" />
66 </when>
67 </conditional>
68 </xml>
69 <xml name="title">
70 <param name="title" type="text" value="plot title" label="Title of plot" />
71 </xml>
72 <xml name="xy_lab">
73 <param name="xlab" type="text" value="title of x-axis" label="Label for x-axis"/>
74 <param name="ylab" type="text" value="title of y-axis" label="Label for y-axis"/>
75 </xml>
76 <xml name="dimensions">
77 <param name="with_output_dim" type="float" value="7" label="width of output" help="in inches" />
78 <param name="height_output_dim" type="float" value="7" label="height of output" help="in inches" />
79 </xml>
80 <xml name="citations">
81 <citations>
82 <citation type="bibtex">@Book{
83 author = {Hadley Wickham},
84 title = {ggplot2: Elegant Graphics for Data Analysis},
85 publisher = {Springer-Verlag New York},
86 year = {2009},
87 isbn = {978-0-387-98140-6},
88 url = {http://ggplot2.org}
89 }
90 </citation>
91 </citations>
92 </xml>
93
94 <xml name="axis_customization" token_label="Advanced - axis title options">
95 <param name="axis_customization" type="select" label="@LABEL@">
96 <option value="default" selected="True">Default</option>
97 <option value="defined">User defined label options</option>
98 </param>
99 <when value="default">
100 <!--Do nothing here -->
101 </when>
102 <when value="defined">
103 <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
104 <param name="color" type="select" label="Color of axis label">
105 <option value="black">Black (default)</option>
106 <option value="red">Red</option>
107 <option value="white">White</option>
108 <option value="blue">Blue</option>
109 <option value="orange">Orange</option>
110 <option value="yellow">Yellow</option>
111 <option value="green">Green</option>
112 <option value="purple">Purple</option>
113 <option value="magenta">Magenta</option>
114 <option value="cyan">Cyan</option>
115 <option value="grey">Grey</option>
116 <option value="gold">Gold</option>
117 </param>
118 <param name="face" type="select" label="Font effect of axis label">
119 <option value="plain">Normal (default)</option>
120 <option value="bold">Bold</option>
121 <option value="italic">Italic</option>
122 </param>
123 </when>
124 </xml>
125
126 <xml name="colors">
127 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
128 <option value="Default">Default color scheme</option>
129 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
130 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
131 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
132 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
133 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
134 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
135 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
136 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
137 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
138 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
139 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
140 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
141 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
142 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
143 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
144 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
145 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
146 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
147 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
148 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
149 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
150 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
151 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
152 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
153 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
154 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
155 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
156 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
157 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
158 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
159 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
160 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
161 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
162 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
163 </param>
164 </xml>
165
166 </macros>