Mercurial > repos > bzeitouni > svdetect
comparison svdetect/circos_graph.xml @ 22:eb65c0fa5542 draft
Uploaded
author | bzeitouni |
---|---|
date | Thu, 12 Jul 2012 12:19:40 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
21:105e78d03f35 | 22:eb65c0fa5542 |
---|---|
1 <tool id="circos_graph" name="Circos"> | |
2 | |
3 <description>plots</description> | |
4 | |
5 <command interpreter="perl">circos/bin/circos | |
6 | |
7 -conf '$circos_config_file' | |
8 -outputdir $__new_file_path__/svdetect | |
9 -outputfile '$outputfile' | |
10 -png | |
11 -out1 '$out1_png' | |
12 | |
13 > '$log_file' | |
14 | |
15 </command> | |
16 | |
17 | |
18 <inputs> | |
19 <param name="graph_name" type="text" size="20" value="graph1" label="Graph name"/> | |
20 | |
21 <param name="karyotype" type="select" format="txt" label="Type of model organism"> | |
22 <option value="data/karyotype.human_hg19.txt">Human (homo sapiens, hs) -hg19-</option> | |
23 <option value="data/karyotype.human.txt">Human (homo sapiens, hs) -hg18-</option> | |
24 <option value="data/2/karyotype.mouse.txt">Mouse (Mus Musculus, mm)</option> | |
25 <option value="data/2/karyotype.dog.txt">Dog (Canis familiaris, cf)</option> | |
26 <option value="data/2/karyotype.rt.txt">Rat (Rattus norvegicus, rn)</option> | |
27 <option value="data/karyotype.yeast.txt">Yeast (Saccharomyces Cerevisiae, sc) -SGD-</option> | |
28 | |
29 </param> | |
30 <param name="chromosomes_units" type="integer" size="50" value="1000000" label="Chromosomes units"/> | |
31 <param name="chromosomes" type="text" size="100" value="" label="List of chromosome names to keep or exclude" help="ex: hs2;hs3 or -hsX;-hsY"> | |
32 <sanitizer> | |
33 <valid initial="string.printable"> | |
34 <add value=";"/> | |
35 </valid> | |
36 </sanitizer> | |
37 </param> | |
38 <param name="link_file" format="segdup" type="data" label="Input link file (.segdup)"/> | |
39 <param name="outputfile" type="text" size="50" value="graph1.circos.png" label="Output image name file (png)"/> | |
40 </inputs> | |
41 | |
42 <outputs> | |
43 <data format="txt" name="log_file" label="${graph_name}.circos.log"/> | |
44 <data format="png" name="out1_png" label="${outputfile}"/> | |
45 </outputs> | |
46 | |
47 | |
48 | |
49 <configfiles> | |
50 <configfile name="ideogram_config_file"> | |
51 | |
52 <ideogram> | |
53 | |
54 <spacing> | |
55 | |
56 default = 5u | |
57 break = 1u | |
58 | |
59 axis_break_at_edge = yes | |
60 axis_break = yes | |
61 axis_break_style = 2 | |
62 | |
63 <break_style 1> | |
64 stroke_color = black | |
65 fill_color = blue | |
66 thickness = 0.25r | |
67 stroke_thickness = 2 | |
68 </break> | |
69 | |
70 <break_style 2> | |
71 stroke_color = black | |
72 stroke_thickness = 3p | |
73 thickness = 1.5r | |
74 </break> | |
75 | |
76 </spacing> | |
77 | |
78 ## thickness (px) of chromosome ideogram | |
79 thickness = 100p | |
80 stroke_thickness = 2 | |
81 ## ideogram border color | |
82 stroke_color = black | |
83 fill = yes | |
84 ## the default chromosome color is set here and any value | |
85 ## defined in the karyotype file overrides it | |
86 fill_color = black | |
87 | |
88 ## fractional radius position of chromosome ideogram within image | |
89 radius = 0.85r | |
90 show_label = yes | |
91 label_with_tag = yes | |
92 label_font = condensedbold | |
93 label_radius = dims(ideogram,radius) + 0.075r | |
94 label_size = 60p | |
95 | |
96 ## cytogenetic bands | |
97 band_stroke_thickness = 2 | |
98 | |
99 ## show_bands determines whether the outline of cytogenetic bands | |
100 ## will be seen | |
101 show_bands = yes | |
102 ## in order to fill the bands with the color defined in the karyotype | |
103 ## file you must set fill_bands | |
104 fill_bands = yes | |
105 | |
106 </ideogram> | |
107 | |
108 </configfile> | |
109 | |
110 <configfile name="ticks_config_file"> | |
111 | |
112 show_ticks = yes | |
113 show_tick_labels = yes | |
114 | |
115 <ticks> | |
116 radius = dims(ideogram,radius_outer) | |
117 multiplier = 1e-6 | |
118 | |
119 <tick> | |
120 spacing = 0.5u | |
121 size = 2p | |
122 thickness = 2p | |
123 color = grey | |
124 show_label = no | |
125 label_size = 12p | |
126 label_offset = 0p | |
127 format = %.2f | |
128 </tick> | |
129 | |
130 <tick> | |
131 spacing = 1u | |
132 size = 3p | |
133 thickness = 2p | |
134 color = dgrey | |
135 show_label = no | |
136 label_size = 12p | |
137 label_offset = 0p | |
138 format = %.2f | |
139 </tick> | |
140 | |
141 <tick> | |
142 spacing = 5u | |
143 size = 5p | |
144 thickness = 2p | |
145 color = black | |
146 show_label = yes | |
147 label_size = 16p | |
148 label_offset = 0p | |
149 format = %d | |
150 </tick> | |
151 | |
152 <tick> | |
153 spacing = 10u | |
154 size = 8p | |
155 thickness = 2p | |
156 color = black | |
157 show_label = yes | |
158 label_size = 20p | |
159 label_offset = 5p | |
160 format = %d | |
161 </tick> | |
162 </ticks> | |
163 </configfile> | |
164 | |
165 | |
166 <configfile name="circos_config_file"> | |
167 <colors> | |
168 <<include etc/colors.conf>> | |
169 </colors> | |
170 | |
171 <fonts> | |
172 <<include etc/fonts.conf>> | |
173 </fonts> | |
174 | |
175 <<include $ideogram_config_file>> | |
176 <<include $ticks_config_file>> | |
177 | |
178 karyotype = $karyotype | |
179 | |
180 <image> | |
181 24bit = yes | |
182 ##png = yes | |
183 ##svg = no | |
184 ## radius of inscribed circle in image | |
185 radius = 1500p | |
186 background = white | |
187 ## by default angle=0 is at 3 o'clock position | |
188 angle_offset = -90 | |
189 #angle_orientation = counterclockwise | |
190 | |
191 auto_alpha_colors = yes | |
192 auto_alpha_steps = 5 | |
193 </image> | |
194 | |
195 chromosomes_units= $chromosomes_units | |
196 | |
197 #if str($chromosomes)=="" | |
198 chromosomes_display_default = yes | |
199 #else | |
200 chromosomes_display_default = no | |
201 chromosomes = $chromosomes | |
202 #end if | |
203 | |
204 <links> | |
205 | |
206 z = 0 | |
207 radius = 0.95r | |
208 bezier_radius = 0.2r | |
209 | |
210 <link segdup> | |
211 show = yes | |
212 color = dgrey_a5 | |
213 thickness = 2 | |
214 file = $link_file | |
215 record_limit = 1000 | |
216 </link> | |
217 | |
218 </links> | |
219 | |
220 | |
221 anglestep = 0.5 | |
222 minslicestep = 10 | |
223 beziersamples = 40 | |
224 debug = no | |
225 warnings = no | |
226 imagemap = no | |
227 | |
228 units_ok = bupr | |
229 units_nounit = n | |
230 </configfile> | |
231 </configfiles> | |
232 | |
233 <help> | |
234 **What it does** | |
235 | |
236 Circos | |
237 | |
238 Manual documentation available at the http://circos.ca/ | |
239 | |
240 | |
241 **Example of link segdup file** | |
242 | |
243 segdup file:: | |
244 | |
245 1 hs1 1077096 1078746 color=red | |
246 1 hs1 1080923 1082805 color=red | |
247 2 hs1 1137684 1137961 color=red | |
248 2 hs3 1138138 1138423 color=red | |
249 3 hs11 1169417 1170000 color=red | |
250 3 hs11 1170025 1170975 color=red | |
251 4 hs11 1222480 1224271 color=green | |
252 4 hs11 1223328 1225675 color=green | |
253 5 hs12 1223336 1225812 color=grey | |
254 5 hs13 1224709 1227633 color=grey | |
255 6 hs11 1223621 1226460 color=red | |
256 6 hs11 1224918 1227633 color=red | |
257 7 hs11 1399510 1401513 color=white | |
258 7 hs11 1401628 1403697 color=white | |
259 8 hs15 1652045 1653746 color=red | |
260 8 hs15 1657167 1658940 color=red | |
261 9 hs11 165333 165887 color=white | |
262 9 hs11 165981 168016 color=white | |
263 10 hs11 1702700 1702841 color=red | |
264 10 hs11 1702903 1703057 color=red | |
265 11 hs11 1912272 1915186 color=white | |
266 11 hs11 1937111 1939824 color=white | |
267 12 hs11 1983211 1983355 color=red | |
268 12 hs11 1983591 1983748 color=red | |
269 13 hs11 2913657 2913898 color=white | |
270 13 hs11 2914048 2914341 color=white | |
271 14 hs11 3090593 3090749 color=purple | |
272 14 hs11 3090709 3090864 color=purple | |
273 15 hs21 3466365 3466434 color=red | |
274 15 hs21 3466554 3466620 color=red | |
275 16 hsX 3603073 3603321 color=white | |
276 16 hsX 3603295 3603520 color=white | |
277 | |
278 | |
279 | |
280 ----- | |
281 | |
282 .. class:: infomark | |
283 | |
284 Contact Bruno Zeitouni (svdetect@curie.fr) for any questions or concerns about the Galaxy implementation of Circos. | |
285 | |
286 | |
287 </help> | |
288 | |
289 </tool> |