Mercurial > repos > moheydarian > ggplot_scatterplot
comparison ggplot_point.xml @ 0:d0564619e245 draft
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author | moheydarian |
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date | Fri, 02 Dec 2016 15:33:31 -0500 |
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-1:000000000000 | 0:d0564619e245 |
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1 <tool id="ggplot_point" name="Scatterplot with ggplott" version="0.1.2"> | |
2 <requirements> | |
3 <requirement type="package">getopt</requirement> | |
4 <requirement type="package">ggplot2</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:" /> | |
8 </stdio> | |
9 <command><![CDATA[ | |
10 Rscript /Users/cmdb/Downloads/Galaxy-wrapper-for-ggplot2-scatterplot-master/ggplotpointscript.R --input "$input1" --title "$title" | |
11 --theme "${theme.theme_selector}" --xplot "$xplot" --yplot "$yplot" --scaling "$scaling.Plot_scaling" --points "$points.pointoptions" --dim "$dimensions.plotdim" --factor "$factor.factoring" --transform "$transformation.transform" --xlab "$xlab" --ylab "$ylab" | |
12 --axistitlecust "$axistitlecustomization.axistitlecust" --axistextcust "$axistextcustomization.axistextcust" | |
13 --plottitlecust "$plottitlecustomization.plottitlecust" --gridlinecust "$gridlinecustomization.gridlinecust" --output "Rplot.pdf" | |
14 #if str( $factor.factoring ) == "Single": | |
15 --factorcol ${factor.factorcol} | |
16 --colors ${factor.colors} | |
17 --colororder ${factor.colororder} | |
18 #elif str( $factor.factoring ) == "Multiple": | |
19 --factorcol ${factor.factorcol} | |
20 --colors=irrelevant | |
21 --colororder=1 | |
22 #else: | |
23 --factorcol=1 | |
24 --colors=irrelevant | |
25 --colororder=1 | |
26 #end if | |
27 | |
28 #if str( $points.pointoptions ) == "Defined": | |
29 --size ${points.size} | |
30 --alpha ${points.alpha} | |
31 --pointcolor ${points.pointcolor} | |
32 #else: | |
33 --size=1 | |
34 --alpha=1 | |
35 --pointcolor=black | |
36 #end if | |
37 | |
38 #if str( $scaling.Plot_scaling ) == "Defined": | |
39 --xaxismin=${scaling.xaxismin} | |
40 --xaxismax=${scaling.xaxismax} | |
41 --yaxismin=${scaling.yaxismin} | |
42 --yaxismax=${scaling.yaxismax} | |
43 #else: | |
44 --xaxismin=0 | |
45 --xaxismax=1 | |
46 --yaxismin=2 | |
47 --yaxismax=3 | |
48 #end if | |
49 | |
50 #if str( $axistitlecustomization.axistitlecust ) == "Defined": | |
51 --axistitlesize ${axistitlecustomization.axistitlesize} | |
52 --axistitlecolor ${axistitlecustomization.axistitlecolor} | |
53 --axistitleface ${axistitlecustomization.axistitleface} | |
54 #else: | |
55 --axistitlesize=12 | |
56 --axistitlecolor=black | |
57 --axistitleface=plain | |
58 #end if | |
59 | |
60 #if str( $axistextcustomization.axistextcust ) == "Defined": | |
61 --axistextsize ${axistextcustomization.axistextsize} | |
62 --axistextcolor ${axistextcustomization.axistextcolor} | |
63 --axistextface ${axistextcustomization.axistextface} | |
64 #else: | |
65 --axistextsize=12 | |
66 --axistextcolor=black | |
67 --axistextface=plain | |
68 #end if | |
69 | |
70 #if str( $plottitlecustomization.plottitlecust ) == "Defined": | |
71 --plottitlesize ${plottitlecustomization.plottitlesize} | |
72 --plottitlecolor ${plottitlecustomization.plottitlecolor} | |
73 --plottitleface ${plottitlecustomization.plottitleface} | |
74 #else: | |
75 --plottitlesize=12 | |
76 --plottitlecolor=black | |
77 --plottitleface=plain | |
78 #end if | |
79 | |
80 #if str( $dimensions.plotdim ) == "Defined": | |
81 --woutputdim ${dimensions.woutputdim} | |
82 --houtputdim ${dimensions.houtputdim} | |
83 #else: | |
84 --woutputdim=7 | |
85 --houtputdim=7 | |
86 #end if | |
87 | |
88 ]]></command> | |
89 <inputs> | |
90 <param name="input1" type="data" format="tabular" label="Input (tabular format)" /> | |
91 <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" /> | |
92 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" /> | |
93 <param name="title" size="30" type="text" value="plot title" label="Title of plot" /> | |
94 <param name="xlab" size="30" type="text" value="title of x-axis" label="Label for x-axis"/> | |
95 <param name="ylab" size="30" type="text" value="title of y-axis" label="Label for y-axis"/> | |
96 <conditional name="points"> | |
97 <param name="pointoptions" type="select" label="Advanced - data point options"> | |
98 <option value="Default" selected="True">Default</option> | |
99 <option value="Defined">User defined point options</option> | |
100 </param> | |
101 <when value="Default"> | |
102 <!--Do nothing here --> | |
103 </when> | |
104 <when value="Defined"> | |
105 <param name="size" size="4" type="float" value="1" label="relative size of points" /> | |
106 <param name="alpha" size="4" type="float" value="1" label="Transparency of points (On a scale of 0-1; 0=transparent, 1=default)" /> | |
107 <param name="pointcolor" type="select" label="Color of data points" > | |
108 <option value="black">Black (default)</option> | |
109 <option value="red">Red</option> | |
110 <option value="white">White</option> | |
111 <option value="blue">Blue</option> | |
112 <option value="orange">Orange</option> | |
113 <option value="yellow">Yellow</option> | |
114 <option value="green">Green</option> | |
115 <option value="purple">Purple</option> | |
116 <option value="magenta">Magenta</option> | |
117 <option value="cyan">Cyan</option> | |
118 <option value="grey">Grey</option> | |
119 <option value="gold">Gold</option> | |
120 </param> | |
121 </when> | |
122 </conditional> | |
123 <conditional name="factor"> | |
124 <param name="factoring" type="select" label="Advanced - plotting multiple groups" > | |
125 <option value="Default" selected="True">No thanks - just plot the data as one group</option> | |
126 <option value="Single">Plot multiple groups of data on one plot</option> | |
127 <option value="Multiple">Plot multiple groups of data on individual plots</option> | |
128 </param> | |
129 <when value="Default"> | |
130 <!--Do nothing here --> | |
131 </when> | |
132 <when value="Single"> | |
133 <param name="factorcol" size="4" type="integer" value="1" label="column differentiating the different groups" /> | |
134 <param name="colors" type="select" label="Color schemes to differentiate your groups" > | |
135 <option value="Default">Default color scheme</option> | |
136 <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option> | |
137 <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option> | |
138 <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option> | |
139 <option value="YlGn">Yellow to green (discrete, max=9 colors)</option> | |
140 <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option> | |
141 <option value="RdPu">Red to purple (discrete, max=9 colors)</option> | |
142 <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option> | |
143 <option value="PuRd">Purple to red (discrete, max=9 colors)</option> | |
144 <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option> | |
145 <option value="PuBu">Purple to blue(discrete, max=9 colors)</option> | |
146 <option value="OrRd">Orange to red (discrete, max=9 colors)</option> | |
147 <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option> | |
148 <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option> | |
149 <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option> | |
150 <option value="GnBu">Green to blue (discrete, max=9 colors)</option> | |
151 <option value="BuPu">Blue to purple (discrete, max=9 colors)</option> | |
152 <option value="BuGn">Blue to green (discrete, max=9 colors)</option> | |
153 <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option> | |
154 <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option> | |
155 <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option> | |
156 <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option> | |
157 <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option> | |
158 <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option> | |
159 <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option> | |
160 <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option> | |
161 <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option> | |
162 <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option> | |
163 <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option> | |
164 <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option> | |
165 <option value="RdGy">Red to grey (discrete, max=11 colors)</option> | |
166 <option value="RdBu">Red to blue (discrete, max=11 colors)</option> | |
167 <option value="PuOr">Purple to orange (discrete, max=11 colors)</option> | |
168 <option value="PRGn">Purple to green (discrete, max=11 colors)</option> | |
169 <option value="BrBG">Brown to teal (discrete, max=11 colors)</option> | |
170 </param> | |
171 <param name="colororder" type="select" label="Reverse color scheme" > | |
172 <option value="1">Default order of color scheme</option> | |
173 <option value="-1">Reverse the order of my color scheme</option> | |
174 </param> | |
175 </when> | |
176 <when value="Multiple"> | |
177 <param name="factorcol" size="4" type="integer" value="1" label="column differentiating the different groups" /> | |
178 </when> | |
179 </conditional> | |
180 <conditional name="transformation"> | |
181 <param name="transform" type="select" label="Advanced - log transformation"> | |
182 <option value="none">Plot the data as it is</option> | |
183 <option value="log2">Log2(value) transform my data</option> | |
184 <option value="log2plus1">Log2(value+1) transform my data</option> | |
185 <option value="log10">Log10(value) transform my data</option> | |
186 <option value="log10plus1">Log10(value+1) transform my data</option> | |
187 </param> | |
188 <when value="none"> | |
189 <!--Do nothing here --> | |
190 </when> | |
191 <when value="log2"> | |
192 <!--Do nothing here --> | |
193 </when> | |
194 <when value="log2plus1"> | |
195 <!--Do nothing here --> | |
196 </when> | |
197 <when value="log10"> | |
198 <!--Do nothing here --> | |
199 </when> | |
200 <when value="log10plus1"> | |
201 <!--Do nothing here --> | |
202 </when> | |
203 </conditional> | |
204 <conditional name="scaling"> | |
205 <param name="Plot_scaling" type="select" label="Advanced - axis scaling"> | |
206 <option value="Automatic" selected="True">Automatic axis scaling</option> | |
207 <option value="Defined">User defined axis scales</option> | |
208 </param> | |
209 <when value="Automatic"> | |
210 <!--Do nothing here --> | |
211 </when> | |
212 <when value="Defined"> | |
213 <param name="xaxismin" size="4" type="integer" value="0" label="minimal range of x-axis" /> | |
214 <param name="xaxismax" size="4" type="integer" value="3" label="maximal range of x-axis" /> | |
215 <param name="yaxismin" size="4" type="integer" value="0" label="minimal range of y-axis" /> | |
216 <param name="yaxismax" size="4" type="integer" value="3" label="maximal range of y-axis" /> | |
217 </when> | |
218 </conditional> | |
219 <conditional name="theme"> | |
220 <param name="theme_selector" type="select" label="Advanced - backgound theme for plot"> | |
221 <option value="bw">Black and white</option> | |
222 <option value="Default">Default (grey)</option> | |
223 </param> | |
224 <when value="bw"/> | |
225 <when value="Default"></when> | |
226 </conditional> | |
227 <conditional name="axistitlecustomization"> | |
228 <param name="axistitlecust" type="select" label="Advanced - axis label options"> | |
229 <option value="Default" selected="True">Default</option> | |
230 <option value="Defined">User defined label options</option> | |
231 </param> | |
232 <when value="Default"> | |
233 <!--Do nothing here --> | |
234 </when> | |
235 <when value="Defined"> | |
236 <param name="axistitlesize" size="4" type="float" value="12" label="Axis label size (default = 12)"/> | |
237 <param name="axistitlecolor" type="select" label="Color of axis label"> | |
238 <option value="black">Black (default)</option> | |
239 <option value="red">Red</option> | |
240 <option value="white">White</option> | |
241 <option value="blue">Blue</option> | |
242 <option value="orange">Orange</option> | |
243 <option value="yellow">Yellow</option> | |
244 <option value="green">Green</option> | |
245 <option value="purple">Purple</option> | |
246 <option value="magenta">Magenta</option> | |
247 <option value="cyan">Cyan</option> | |
248 <option value="grey">Grey</option> | |
249 <option value="gold">Gold</option> | |
250 </param> | |
251 <param name="axistitleface" size="4" type="select" label="Font effect of axis label"> | |
252 <option value="plain">Normal (default)</option> | |
253 <option value="bold">Bold</option> | |
254 <option value="italic">Italic</option> | |
255 </param> | |
256 </when> | |
257 </conditional> | |
258 <conditional name="axistextcustomization"> | |
259 <param name="axistextcust" type="select" label="Advanced - axis text options"> | |
260 <option value="Default" selected="True">Default</option> | |
261 <option value="Defined">User defined axis text options</option> | |
262 </param> | |
263 <when value="Default"> | |
264 <!--Do nothing here --> | |
265 </when> | |
266 <when value="Defined"> | |
267 <param name="axistextsize" size="4" type="float" value="12" label="Axis text size (default = 12)"/> | |
268 <param name="axistextcolor" type="select" label="Color of axis text"> | |
269 <option value="black">Black (default)</option> | |
270 <option value="red">Red</option> | |
271 <option value="white">White</option> | |
272 <option value="blue">Blue</option> | |
273 <option value="orange">Orange</option> | |
274 <option value="yellow">Yellow</option> | |
275 <option value="green">Green</option> | |
276 <option value="purple">Purple</option> | |
277 <option value="magenta">Magenta</option> | |
278 <option value="cyan">Cyan</option> | |
279 <option value="grey">Grey</option> | |
280 <option value="gold">Gold</option> | |
281 </param> | |
282 <param name="axistextface" size="4" type="select" label="Font effect of axis text"> | |
283 <option value="plain">Normal (default)</option> | |
284 <option value="bold">Bold</option> | |
285 <option value="italic">Italic</option> | |
286 </param> | |
287 </when> | |
288 </conditional> | |
289 <conditional name="plottitlecustomization"> | |
290 <param name="plottitlecust" type="select" label="Advanced - Plot title options"> | |
291 <option value="Default" selected="True">Default</option> | |
292 <option value="Defined">User defined plot title options</option> | |
293 </param> | |
294 <when value="Default"> | |
295 <!--Do nothing here --> | |
296 </when> | |
297 <when value="Defined"> | |
298 <param name="plottitlesize" size="4" type="float" value="12" label="Plot title size (default = 12)"/> | |
299 <param name="plottitlecolor" type="select" label="Color of plot title"> | |
300 <option value="black">Black (default)</option> | |
301 <option value="red">Red</option> | |
302 <option value="white">White</option> | |
303 <option value="blue">Blue</option> | |
304 <option value="orange">Orange</option> | |
305 <option value="yellow">Yellow</option> | |
306 <option value="green">Green</option> | |
307 <option value="purple">Purple</option> | |
308 <option value="magenta">Magenta</option> | |
309 <option value="cyan">Cyan</option> | |
310 <option value="grey">Grey</option> | |
311 <option value="gold">Gold</option> | |
312 </param> | |
313 <param name="plottitleface" size="4" type="select" label="Font effect of plot title"> | |
314 <option value="plain">Normal (default)</option> | |
315 <option value="bold">Bold</option> | |
316 <option value="italic">Italic</option> | |
317 </param> | |
318 </when> | |
319 </conditional> | |
320 <conditional name="gridlinecustomization"> | |
321 <param name="gridlinecust" type="select" label="Advanced - grid lines"> | |
322 <option value="Default">Default grid lines</option> | |
323 <option value="hidemajor">Hide major grid lines</option> | |
324 <option value="hideminor">Hide minor grid lines</option> | |
325 <option value="hideboth">Hide major and minor grid lines</option> | |
326 </param> | |
327 <when value="Default"> | |
328 <!--Do nothing here --> | |
329 </when> | |
330 <when value="hidemajor"> | |
331 <!--Do nothing here --> | |
332 </when> | |
333 <when value="hideminor"> | |
334 <!--Do nothing here --> | |
335 </when> | |
336 <when value="hideboth"> | |
337 <!--Do nothing here --> | |
338 </when> | |
339 </conditional> | |
340 <conditional name="dimensions"> | |
341 <param name="plotdim" type="select" label="Advanced - output dimensions"> | |
342 <option value="Default" selected="True">Default</option> | |
343 <option value="Defined">User defined output dimensions</option> | |
344 </param> | |
345 <when value="Default"> | |
346 <!--Do nothing here --> | |
347 </when> | |
348 <when value="Defined"> | |
349 <param name="woutputdim" size="4" type="float" value="7" label="width of output (inches)" /> | |
350 <param name="houtputdim" size="4" type="float" value="7" label="height of output (inches)" /> | |
351 </when> | |
352 </conditional> | |
353 </inputs> | |
354 <outputs> | |
355 <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> --> | |
356 <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/> | |
357 </outputs> | |
358 <tests> | |
359 <test> | |
360 <param name="input1" value="input.txt"/> | |
361 <output name="output1" file="Rplot.pdf"/> | |
362 </test> | |
363 </tests> | |
364 <help><![CDATA[ | |
365 This tool will generate a scatterplot representing data from two groups/conditions. | |
366 | |
367 The input data should be in tabular format and the user can determine which groups (columns) to plot. | |
368 | |
369 Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups". | |
370 | |
371 Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user! | |
372 | |
373 The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "Advanced - output dimensions" | |
374 | |
375 | |
376 | |
377 | |
378 Please report issues at: https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot | |
379 ]]></help> | |
380 <citations> | |
381 <citation type="bibtex"> | |
382 @misc{renameTODO, | |
383 author = {8.5.2016, FirstTODO}, | |
384 year = {TODO}, | |
385 title = {TODO}, | |
386 url = {http://docs.ggplot2.org/current/geom_point.html}, | |
387 }</citation> | |
388 </citations> | |
389 </tool> |