Mercurial > repos > bzeitouni > svdetect
comparison SVDetect_r0.8b_galaxy/svdetect/circos_graph.xml @ 28:091714bd75a0 draft default tip
new release r0.8b
author | bzeitouni |
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date | Tue, 22 Jan 2013 06:20:22 -0500 |
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27:c284618dd8da | 28:091714bd75a0 |
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1 <tool id="circos_graph" name="Circos" version="1.1.0"> | |
2 | |
3 <description>plots</description> | |
4 | |
5 <command interpreter="perl">circos/bin/circos | |
6 | |
7 -conf '$circos_config_file' | |
8 -outputfile '${outputfile}.dat' | |
9 -png | |
10 | |
11 > '$log_file' | |
12 | |
13 ; | |
14 | |
15 rm '$outputfile'; ln -s '${outputfile}.png' '$outputfile' | |
16 | |
17 </command> | |
18 | |
19 | |
20 <inputs> | |
21 <param name="graph_name" type="text" size="20" value="graph1" label="Graph name"/> | |
22 | |
23 <param name="karyotype" type="select" format="txt" label="Type of model organism"> | |
24 <option value="data/karyotype.human_hg19.txt">Human (homo sapiens, hs) -hg19-</option> | |
25 <option value="data/karyotype.human.txt">Human (homo sapiens, hs) -hg18-</option> | |
26 <option value="data/2/karyotype.mouse.txt">Mouse (Mus Musculus, mm)</option> | |
27 <option value="data/2/karyotype.dog.txt">Dog (Canis familiaris, cf)</option> | |
28 <option value="data/2/karyotype.rt.txt">Rat (Rattus norvegicus, rn)</option> | |
29 <option value="data/karyotype.yeast.txt">Yeast (Saccharomyces Cerevisiae, sc) -SGD-</option> | |
30 | |
31 </param> | |
32 <param name="chromosomes_units" type="integer" size="50" value="1000000" label="Chromosomes units"/> | |
33 <param name="chromosomes" type="text" size="100" value="" label="List of chromosome names to keep or exclude" help="ex: hs2;hs3 or -hsX;-hsY"> | |
34 <sanitizer> | |
35 <valid initial="string.printable"> | |
36 <add value=";"/> | |
37 </valid> | |
38 </sanitizer> | |
39 </param> | |
40 <param name="link_file" format="segdup" type="data" label="Input link file (.segdup)"/> | |
41 </inputs> | |
42 | |
43 <outputs> | |
44 <data format="txt" name="log_file" label="${graph_name}.circos.log"/> | |
45 <data format="png" name="outputfile" label="${graph_name}.png"/> | |
46 </outputs> | |
47 | |
48 | |
49 | |
50 <configfiles> | |
51 <configfile name="ideogram_config_file"> | |
52 | |
53 <ideogram> | |
54 | |
55 <spacing> | |
56 | |
57 default = 5u | |
58 break = 1u | |
59 | |
60 axis_break_at_edge = yes | |
61 axis_break = yes | |
62 axis_break_style = 2 | |
63 | |
64 <break_style 1> | |
65 stroke_color = black | |
66 fill_color = blue | |
67 thickness = 0.25r | |
68 stroke_thickness = 2 | |
69 </break> | |
70 | |
71 <break_style 2> | |
72 stroke_color = black | |
73 stroke_thickness = 3p | |
74 thickness = 1.5r | |
75 </break> | |
76 | |
77 </spacing> | |
78 | |
79 ## thickness (px) of chromosome ideogram | |
80 thickness = 100p | |
81 stroke_thickness = 2 | |
82 ## ideogram border color | |
83 stroke_color = black | |
84 fill = yes | |
85 ## the default chromosome color is set here and any value | |
86 ## defined in the karyotype file overrides it | |
87 fill_color = black | |
88 | |
89 ## fractional radius position of chromosome ideogram within image | |
90 radius = 0.85r | |
91 show_label = yes | |
92 label_with_tag = yes | |
93 label_font = condensedbold | |
94 label_radius = dims(ideogram,radius) + 0.075r | |
95 label_size = 60p | |
96 | |
97 ## cytogenetic bands | |
98 band_stroke_thickness = 2 | |
99 | |
100 ## show_bands determines whether the outline of cytogenetic bands | |
101 ## will be seen | |
102 show_bands = yes | |
103 ## in order to fill the bands with the color defined in the karyotype | |
104 ## file you must set fill_bands | |
105 fill_bands = yes | |
106 | |
107 </ideogram> | |
108 | |
109 </configfile> | |
110 | |
111 <configfile name="ticks_config_file"> | |
112 | |
113 show_ticks = yes | |
114 show_tick_labels = yes | |
115 | |
116 <ticks> | |
117 radius = dims(ideogram,radius_outer) | |
118 multiplier = 1e-6 | |
119 | |
120 <tick> | |
121 spacing = 0.5u | |
122 size = 2p | |
123 thickness = 2p | |
124 color = grey | |
125 show_label = no | |
126 label_size = 12p | |
127 label_offset = 0p | |
128 format = %.2f | |
129 </tick> | |
130 | |
131 <tick> | |
132 spacing = 1u | |
133 size = 3p | |
134 thickness = 2p | |
135 color = dgrey | |
136 show_label = no | |
137 label_size = 12p | |
138 label_offset = 0p | |
139 format = %.2f | |
140 </tick> | |
141 | |
142 <tick> | |
143 spacing = 5u | |
144 size = 5p | |
145 thickness = 2p | |
146 color = black | |
147 show_label = yes | |
148 label_size = 16p | |
149 label_offset = 0p | |
150 format = %d | |
151 </tick> | |
152 | |
153 <tick> | |
154 spacing = 10u | |
155 size = 8p | |
156 thickness = 2p | |
157 color = black | |
158 show_label = yes | |
159 label_size = 20p | |
160 label_offset = 5p | |
161 format = %d | |
162 </tick> | |
163 </ticks> | |
164 </configfile> | |
165 | |
166 | |
167 <configfile name="circos_config_file"> | |
168 <colors> | |
169 <<include etc/colors.conf>> | |
170 </colors> | |
171 | |
172 <fonts> | |
173 <<include etc/fonts.conf>> | |
174 </fonts> | |
175 | |
176 <<include $ideogram_config_file>> | |
177 <<include $ticks_config_file>> | |
178 | |
179 karyotype = $karyotype | |
180 | |
181 <image> | |
182 24bit = yes | |
183 ##png = yes | |
184 ##svg = no | |
185 ## radius of inscribed circle in image | |
186 radius = 1500p | |
187 background = white | |
188 ## by default angle=0 is at 3 o'clock position | |
189 angle_offset = -90 | |
190 #angle_orientation = counterclockwise | |
191 | |
192 auto_alpha_colors = yes | |
193 auto_alpha_steps = 5 | |
194 </image> | |
195 | |
196 chromosomes_units= $chromosomes_units | |
197 | |
198 #if str($chromosomes)=="" | |
199 chromosomes_display_default = yes | |
200 #else | |
201 chromosomes_display_default = no | |
202 chromosomes = $chromosomes | |
203 #end if | |
204 | |
205 <links> | |
206 | |
207 z = 0 | |
208 radius = 0.95r | |
209 bezier_radius = 0.2r | |
210 | |
211 <link segdup> | |
212 show = yes | |
213 color = dgrey_a5 | |
214 thickness = 2 | |
215 file = $link_file | |
216 record_limit = 1000 | |
217 </link> | |
218 | |
219 </links> | |
220 | |
221 | |
222 anglestep = 0.5 | |
223 minslicestep = 10 | |
224 beziersamples = 40 | |
225 debug = no | |
226 warnings = no | |
227 imagemap = no | |
228 | |
229 units_ok = bupr | |
230 units_nounit = n | |
231 </configfile> | |
232 </configfiles> | |
233 | |
234 <help> | |
235 **What it does** | |
236 | |
237 Circos | |
238 | |
239 Manual documentation available at the http://circos.ca/ | |
240 | |
241 | |
242 **Example of link segdup file** | |
243 | |
244 segdup file:: | |
245 | |
246 1 hs1 1077096 1078746 color=red | |
247 1 hs1 1080923 1082805 color=red | |
248 2 hs1 1137684 1137961 color=red | |
249 2 hs3 1138138 1138423 color=red | |
250 3 hs11 1169417 1170000 color=red | |
251 3 hs11 1170025 1170975 color=red | |
252 4 hs11 1222480 1224271 color=green | |
253 4 hs11 1223328 1225675 color=green | |
254 5 hs12 1223336 1225812 color=grey | |
255 5 hs13 1224709 1227633 color=grey | |
256 6 hs11 1223621 1226460 color=red | |
257 6 hs11 1224918 1227633 color=red | |
258 7 hs11 1399510 1401513 color=white | |
259 7 hs11 1401628 1403697 color=white | |
260 8 hs15 1652045 1653746 color=red | |
261 8 hs15 1657167 1658940 color=red | |
262 9 hs11 165333 165887 color=white | |
263 9 hs11 165981 168016 color=white | |
264 10 hs11 1702700 1702841 color=red | |
265 10 hs11 1702903 1703057 color=red | |
266 11 hs11 1912272 1915186 color=white | |
267 11 hs11 1937111 1939824 color=white | |
268 12 hs11 1983211 1983355 color=red | |
269 12 hs11 1983591 1983748 color=red | |
270 13 hs11 2913657 2913898 color=white | |
271 13 hs11 2914048 2914341 color=white | |
272 14 hs11 3090593 3090749 color=purple | |
273 14 hs11 3090709 3090864 color=purple | |
274 15 hs21 3466365 3466434 color=red | |
275 15 hs21 3466554 3466620 color=red | |
276 16 hsX 3603073 3603321 color=white | |
277 16 hsX 3603295 3603520 color=white | |
278 | |
279 | |
280 | |
281 ----- | |
282 | |
283 .. class:: infomark | |
284 | |
285 Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of Circos. | |
286 | |
287 | |
288 </help> | |
289 | |
290 </tool> |