Mercurial > repos > iuc > ggplot2_pca

comparison macros.xml @ 0:e148543c622e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
author iuc
date Mon, 11 Jun 2018 16:03:49 -0400
parents
children 4c8be8b39dae
comparison
equal deleted inserted replaced
-1:000000000000 0:e148543c622e
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 $adv.transform == "log2"
21 input["value"] <- log2(input["value"])
22 #elif $adv.transform == "log2plus1"
23 input["value"] <- log2(input["value"]+1)
24 #elif $adv.transform == "log10"
25 input["value"] <- log10(input["value"])
26 #elif $adv.transform == "log10plus1"
27 input["value"] <- log10(input["value"]+1)
28 #end if
29 ]]></token>
30
31 <token name="@XY_SCALING@"><![CDATA[
32 #Choose between automatically scaled x and y axis or user defined
33 #if $adv.scaling.plot_scaling == "Automatic"
34 gg_scalex = NULL
35 gg_scaley = NULL
36 #else
37 gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
38 gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
39 cat("\n xaxismin: ", $adv.scaling.xaxismin)
40 cat("\n xaxismax: ", $adv.scaling.xaxismax)
41 cat("\n yaxismin: ", $adv.scaling.yaxismin)
42 cat("\n yaxismax: ", $adv.scaling.yaxismax)
43 #end if
44 ]]></token>
45
46 <token name="@THEME@"><![CDATA[
47 ## Choose theme for plot
48 #if $adv.theme == "bw"
49 gg_theme = theme_bw()
50 #else
51 gg_theme = NULL
52 #end if
53 ]]></token>
54
55 <token name="@LEGEND@"><![CDATA[
56 ## Show/hide legend
57 #if $adv.legend == "yes"
58 gg_legend = theme(legend.position="right")
59 #else
60 gg_legend = theme(legend.position="none")
61 cat("\n no legend")
62 #end if
63 ]]></token>
64 <token name="@SAVE_OUTPUT@"><![CDATA[
65 ## output options need to be in out section
66 gg_width <- as.double('$out.width_output_dim')
67 gg_height <- as.double('$out.height_output_dim')
68 gg_unit <- '$out.unit_output_dim'
69 gg_dpi <- as.double('$out.dpi_output_dim')
70 gg_add_device <- '$out.additional_output_format'
71 output1 <- '$output1'
72 output2 <- '$output2'
73
74 ## ggsave to png
75 ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
76 if(gg_add_device != "none"){
77 ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
78 }
79 ]]></token>
80 <xml name="read_complex_input">
81 <param name="input1" type="data" format="tabular" label="Select table"/>
82 <conditional name="inputdata">
83 <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
84 <option value="with_header" selected="true">Dataset with header</option>
85 <option value="with_rownames">Dataset with row names</option>
86 <option value="with_header_rownames">Dataset with header and row names</option>
87 <option value="no_header_rownames">Dataset without header or row names</option>
88 </param>
89 <when value="with_header">
90 <param name="header" type="hidden" value="TRUE"/>
91 <param name="row_names_index" type="hidden" value="0"/>
92 <param name="sample_name_orientation" type="select" display="radio" multiple="false" label="Sample names orientation" help="Default horizontal: header names are interpreted as sample names">
93 <option value="TRUE" selected="true">horizontal</option>
94 <option value="FALSE">vertial</option>
95 </param>
96 </when>
97 <when value="with_rownames">
98 <param name="header" type="hidden" value="FALSE"/>
99 <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
100 <param name="sample_name_orientation" type="select" display="radio" label="Sample names orientation" help="default vertial: row names are interpreted as sample names">
101 <option value="TRUE">horizontal</option>
102 <option value="FALSE" selected="true">vertial</option>
103 </param>
104 </when>
105 <when value="with_header_rownames">
106 <param name="header" type="hidden" value="TRUE"/>
107 <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
108 <param name="sample_name_orientation" type="select" label="Sample names orientation" display="radio" multiple="false" help="deside whether header names or row names are interpreted as sample names">
109 <option value="TRUE" selected="true">horizontal</option>
110 <option value="FALSE">vertial</option>
111 </param>
112 </when>
113 <when value="no_header_rownames">
114 <param name="header" type="hidden" value="FALSE"/>
115 <param name="row_names_index" type="hidden" value="0"/>
116 <param name="sample_name_orientation" type="hidden" value="TRUE"/>
117 </when>
118 </conditional>
119 </xml>
120 <xml name="transform">
121 <param name="transform" type="select" label="Data transformation">
122 <option value="none">Plot the data as it is</option>
123 <option value="log2">Log2(value) transform my data</option>
124 <option value="log2plus1">Log2(value+1) transform my data</option>
125 <option value="log10">Log10(value) transform my data</option>
126 <option value="log10plus1">Log10(value+1) transform my data</option>
127 </param>
128 </xml>
129 <xml name="xy_scaling">
130 <conditional name="scaling">
131 <param name="plot_scaling" type="select" label="Axis scaling">
132 <option value="Automatic" selected="true">Automatic axis scaling</option>
133 <option value="Defined">User-defined axis scales</option>
134 </param>
135 <when value="Automatic">
136 <!--Do nothing here -->
137 </when>
138 <when value="Defined">
139 <param name="xaxismin" type="integer" value="0" label="minimal range of x-axis" />
140 <param name="xaxismax" type="integer" value="3" label="maximal range of x-axis" />
141 <param name="yaxismin" type="integer" value="0" label="minimal range of y-axis" />
142 <param name="yaxismax" type="integer" value="3" label="maximal range of y-axis" />
143 </when>
144 </conditional>
145 </xml>
146 <xml name="title">
147 <param name="title" type="text" value="" label="Plot title">
148 <!--<sanitizer sanitize="false"/> -->
149 </param>
150 </xml>
151 <xml name="xy_lab">
152 <param name="xlab" type="text" value="title of x-axis" label="Label for x axis">
153 <sanitizer sanitize="false"/>
154 </param>
155 <param name="ylab" type="text" value="title of y-axis" label="Label for y axis">
156 <sanitizer sanitize="false"/>
157 </param>
158 </xml>
159 <xml name="legend">
160 <param name="legend" type="select" label="Legend options">
161 <option value="yes">Include legend on plot</option>
162 <option value="no">Hide legend</option>
163 </param>
164 </xml>
165 <xml name="theme">
166 <param name="theme" type="select" label="Backgound theme for plot">
167 <option value="bw">Black and white</option>
168 <option value="Default">Default (grey)</option>
169 </param>
170 </xml>
171 <xml name="dimensions">
172 <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="default inches">
173 <option value="in" selected="true">Inches (in)</option>
174 <option value="cm">Centimeters (cm)</option>
175 <option value="mm">Millimeters (mm)</option>
176 </param>
177 <param name="width_output_dim" type="float" value="7" label="width of output"/>
178 <param name="height_output_dim" type="float" value="7" label="height of output"/>
179 <param name="dpi_output_dim" type="float" value="300" label="dpi of output" help="Plot resolution. Applies only to raster output types."/>
180 <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format">
181 <option value="none" selected="true">only PNG</option>
182 <option value="pdf">PDF</option>
183 <option value="svg">SVG</option>
184 <option value="eps">EPS</option>
185 <option value="ps">PS</option>
186 <option value="tex">TEX (pictex)</option>
187 <option value="jpeg">JPEG</option>
188 <option value="tiff">TIFF</option>
189 <option value="bmp">BMP</option>
190 </param>
191 </xml>
192 <xml name="citations">
193 <citations>
194 <citation type="bibtex">@book{wickham2009ggplot2,
195 author = {Hadley Wickham},
196 title = {ggplot2: Elegant Graphics for Data Analysis},
197 publisher = {Springer-Verlag New York},
198 year = {2009},
199 isbn = {978-0-387-98140-6},
200 url = {http://ggplot2.org},
201 }
202 </citation>
203 <yield />
204 </citations>
205 </xml>
206 <xml name="axis_customization" token_label="Axis title options">
207 <param name="axis_customization" type="select" label="@LABEL@">
208 <option value="default" selected="true">Default</option>
209 <option value="defined">User defined label options</option>
210 </param>
211 <when value="default">
212 <!--Do nothing here -->
213 </when>
214 <when value="defined">
215 <param name="size" type="float" value="12" label="Axis label size (default = 12)"/>
216 <param name="color" type="select" label="Color of axis label">
217 <option value="black">Black (default)</option>
218 <option value="red">Red</option>
219 <option value="white">White</option>
220 <option value="blue">Blue</option>
221 <option value="orange">Orange</option>
222 <option value="yellow">Yellow</option>
223 <option value="green">Green</option>
224 <option value="purple">Purple</option>
225 <option value="magenta">Magenta</option>
226 <option value="cyan">Cyan</option>
227 <option value="grey">Grey</option>
228 <option value="gold">Gold</option>
229 </param>
230 <param name="face" type="select" label="Font effect of axis label">
231 <option value="plain">Normal (default)</option>
232 <option value="bold">Bold</option>
233 <option value="italic">Italic</option>
234 </param>
235 </when>
236 </xml>
237 <xml name="colors">
238 <param name="colors" type="select" label="Color schemes to differentiate your groups" >
239 <option value="Default">Default color scheme</option>
240 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option>
241 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option>
242 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option>
243 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option>
244 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option>
245 <option value="RdPu">Red to purple (discrete, max=9 colors)</option>
246 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option>
247 <option value="PuRd">Purple to red (discrete, max=9 colors)</option>
248 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option>
249 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option>
250 <option value="OrRd">Orange to red (discrete, max=9 colors)</option>
251 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option>
252 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option>
253 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option>
254 <option value="GnBu">Green to blue (discrete, max=9 colors)</option>
255 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option>
256 <option value="BuGn">Blue to green (discrete, max=9 colors)</option>
257 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option>
258 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option>
259 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option>
260 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option>
261 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option>
262 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option>
263 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option>
264 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option>
265 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option>
266 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option>
267 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option>
268 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option>
269 <option value="RdGy">Red to grey (discrete, max=11 colors)</option>
270 <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
271 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
272 <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
273 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
274 </param>
275 </xml>
276 <xml name="additional_output">
277 <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>
278 <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
279 <change_format>
280 <when input="out.additional_output_format" value="svg" format="svg" />
281 <when input="out.additional_output_format" value="eps" format="eps" />
282 <when input="out.additional_output_format" value="ps" format="ps" />
283 <when input="out.additional_output_format" value="tex" format="txt" />
284 <when input="out.additional_output_format" value="jpeg" format="jpg" />
285 <when input="out.additional_output_format" value="tiff" format="tiff" />
286 <when input="out.additional_output_format" value="bmp" format="bmp" />
287 </change_format>
288 <filter>out['additional_output_format'] != "none"</filter>
289 </data>
290 </xml>
291 </macros>