Mercurial > repos > iuc > circos
comparison macros.xml @ 2:014a21767ac4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author | iuc |
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date | Tue, 17 Sep 2019 16:54:57 -0400 |
parents | ae9994cf526f |
children | fd59d783248a |
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1:ae9994cf526f | 2:014a21767ac4 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <macros> | 2 <macros> |
3 <token name="@WRAPPER_VERSION@">0.9-RC2</token> | 3 <token name="@CIRCOS_VERSION@">0.69.8</token> |
4 | |
5 <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy1</token> | |
6 | |
4 <xml name="requirements"> | 7 <xml name="requirements"> |
5 <requirements> | 8 <requirements> |
6 <requirement type="package" version="0.69.5">circos</requirement> | 9 <requirement type="package" version="@CIRCOS_VERSION@">circos</requirement> |
7 <requirement type="package" version="2.7">python</requirement> | 10 <requirement type="package" version="2.7">python</requirement> |
8 <requirement type="package" version="0.6.4">bcbiogff</requirement> | 11 <requirement type="package" version="0.6.4">bcbiogff</requirement> |
9 <requirement type="package" version="1.70">biopython</requirement> | 12 <requirement type="package" version="1.70">biopython</requirement> |
13 <requirement type="package" version="0.3.13">pybigwig</requirement> | |
14 <requirement type="package" version="0.23">circos-tools</requirement> | |
15 <yield /> | |
10 </requirements> | 16 </requirements> |
11 </xml> | 17 </xml> |
18 | |
19 <token name="@UTILS@"> | |
20 #def circosColor($value) | |
21 #set $value = str($value) | |
22 #set $r = int($value[1:3], 16) | |
23 #set $g = int($value[3:5], 16) | |
24 #set $b = int($value[5:], 16) | |
25 $r, $g, $b | |
26 #end def | |
27 #def circosColorAlpha($value, $alpha) | |
28 #set $value = str($value) | |
29 #set $r = int($value[1:3], 16) | |
30 #set $g = int($value[3:5], 16) | |
31 #set $b = int($value[5:], 16) | |
32 #set $a = float($alpha) | |
33 $r, $g, $b, $a | |
34 #end def | |
35 #def chromosomesToOrder($value) | |
36 #set $q = ','.join([x if ':' not in x else x[x:x.index(':')] for x in str($value).split(';')]) | |
37 $q | |
38 #end def | |
39 </token> | |
12 | 40 |
13 <xml name="citations"> | 41 <xml name="citations"> |
14 <citations> | 42 <citations> |
15 <citation type="doi">10.1101/gr.092759.109</citation> | 43 <citation type="doi">10.1101/gr.092759.109</citation> |
16 </citations> | 44 </citations> |
45 </xml> | |
46 | |
47 <xml name="stroke_opts"> | |
48 <expand macro="circos_color_alpha" name="stroke_color" value="#000000" label="Stroke Color"/> | |
49 <param name="stroke_thickness" type="integer" value="1" label="Stroke Thickness"/> | |
50 </xml> | |
51 | |
52 <xml name="minmax"> | |
53 <conditional name="minmax"> | |
54 <param name="minmax_select" type="select" label="Minimum / maximum options"> | |
55 <option value="yes">Supply min/max values</option> | |
56 <option value="no" selected="true">Plot all values</option> | |
57 </param> | |
58 <when value="yes"> | |
59 <param name="min_value" type="float" value="1.0" label="Minimum value" /> | |
60 <param name="max_value" type="float" value="5.0" label="Maximum value" /> | |
61 </when> | |
62 <when value="no"> | |
63 </when> | |
64 </conditional> | |
17 </xml> | 65 </xml> |
18 | 66 |
19 <xml name="circos_color" | 67 <xml name="circos_color" |
20 token_label="Color" | 68 token_label="Color" |
21 token_name="color" | 69 token_name="color" |
29 </valid> | 77 </valid> |
30 </sanitizer> | 78 </sanitizer> |
31 </param> | 79 </param> |
32 </xml> | 80 </xml> |
33 | 81 |
34 <xml name="auto_color" | 82 <xml name="circos_color_alpha" |
83 token_label="Color" | |
35 token_name="color" | 84 token_name="color" |
36 token_label="Color"> | 85 token_value="#000000" |
37 <conditional name="@NAME@" label="@LABEL@"> | 86 token_help="" |
38 <param name="@NAME@_select" type="select" label="@LABEL@"> | 87 > |
39 <option value="automatic" selected="true">Automatic Selection</option> | 88 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@"> |
40 <option value="manual">Manual Specification</option> | 89 <sanitizer> |
41 </param> | 90 <valid initial="string.letters,string.digits"> |
42 <when value="automatic"> | 91 <add value="#" /> |
43 </when> | 92 </valid> |
44 <when value="manual"> | 93 </sanitizer> |
45 <param name="@NAME@" label="@LABEL@" type="color" value="#000000"> | 94 </param> |
46 <sanitizer> | 95 <param name="@NAME@_alpha" type="float" label="Transparency" value="1" min="0" max="1" help="1 = fully opaque, 0 = fully transparent"/> |
47 <valid initial="string.letters,string.digits"> | |
48 <add value="#" /> | |
49 </valid> | |
50 </sanitizer> | |
51 </param> | |
52 </when> | |
53 </conditional> | |
54 </xml> | 96 </xml> |
55 | 97 |
56 <xml name="brewer_scale" | 98 <xml name="brewer_scale" |
57 token_name="color" | 99 token_name="color" |
58 token_label="Color"> | 100 token_label="Color"> |
87 <option value="rdylgn-15-div">Diverging: Red - Yellow - Green</option> | 129 <option value="rdylgn-15-div">Diverging: Red - Yellow - Green</option> |
88 <option value="spectral-15-div">Diverging: Spectral</option> | 130 <option value="spectral-15-div">Diverging: Spectral</option> |
89 | 131 |
90 <option value="accent-8-qual">Qualitative: Accent</option> | 132 <option value="accent-8-qual">Qualitative: Accent</option> |
91 <option value="dark2-8-qual">Qualitative: Dark2</option> | 133 <option value="dark2-8-qual">Qualitative: Dark2</option> |
92 <option value="paired-12-qual">Qualitative: Paired</option> | 134 <option value="paired-12-qual" selected="true">Qualitative: Paired</option> |
93 <option value="pastel1-9-qual">Qualitative: Pastel1</option> | 135 <option value="pastel1-9-qual">Qualitative: Pastel1</option> |
94 <option value="pastel2-8-qual">Qualitative: Pastel2</option> | 136 <option value="pastel2-8-qual">Qualitative: Pastel2</option> |
95 <option value="set1-9-qual">Qualitative: Set1</option> | 137 <option value="set1-9-qual">Qualitative: Set1</option> |
96 <option value="set2-8-qual">Qualitative: Set2</option> | 138 <option value="set2-8-qual">Qualitative: Set2</option> |
97 <option value="set3-12-qual">Qualitative: Set3</option> | 139 <option value="set3-12-qual">Qualitative: Set3</option> |
98 </param> | 140 </param> |
99 </xml> | 141 </xml> |
100 | 142 |
143 <xml name="font_select" | |
144 token_normal="true" | |
145 token_bold="false"> | |
146 <param name="font" type="select" label="Font"> | |
147 <option value="light">light</option> | |
148 <option value="normal" selected="@NORMAL@">normal</option> | |
149 <option value="default">default</option> | |
150 <option value="semibold">semibold</option> | |
151 <option value="bold" selected="@BOLD@">bold</option> | |
152 <option value="italic">italic</option> | |
153 <option value="bolditalic">bolditalic</option> | |
154 <option value="italicbold">italicbold</option> | |
155 </param> | |
156 </xml> | |
157 | |
101 <xml name="axes"> | 158 <xml name="axes"> |
102 <section name="sec_axes" title="Axes"> | 159 <section name="sec_axes" title="Axes"> |
103 <repeat name="axes" title="Axis"> | 160 <repeat name="axes" title="Axis"> |
104 <param name="y0" type="float" value="0.0" label="Inside Radius (y0)" help="This is relative to the subplot you are currently in."/> | 161 <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> |
105 <param name="y1" type="float" value="1" label="Outside Radius (y1)" help="This is relative to the subplot you are currently in."/> | 162 <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> |
106 | 163 |
107 <expand macro="circos_color"/> | 164 <expand macro="circos_color"/> |
108 <param name="thickness" type="integer" value="1" label="Thickness"/> | 165 <param name="thickness" type="integer" value="1" label="Thickness"/> |
109 <param name="spacing" type="float" value="0.1" label="Spacing" help="Relative spacing between each concentric arc"/> | 166 <param name="spacing" type="float" value="0.1" label="Spacing" help="Relative spacing between each concentric arc"/> |
110 </repeat> | 167 </repeat> |
112 </xml> | 169 </xml> |
113 | 170 |
114 <xml name="backgrounds"> | 171 <xml name="backgrounds"> |
115 <section name="sec_bkgs" title="Backgrounds"> | 172 <section name="sec_bkgs" title="Backgrounds"> |
116 <repeat name="backgrounds" title="Background"> | 173 <repeat name="backgrounds" title="Background"> |
117 <param name="y0" type="float" value="0.0" label="Inside Radius (y0)" help="This is relative to the subplot you are currently in."/> | 174 <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> |
118 <param name="y1" type="float" value="1" label="Outside Radius (y1)" help="This is relative to the subplot you are currently in."/> | 175 <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/> |
119 <expand macro="circos_color"/> | 176 <expand macro="circos_color"/> |
120 </repeat> | 177 </repeat> |
121 </section> | 178 </section> |
122 </xml> | 179 </xml> |
123 | 180 |
128 <conditional name="application"> | 185 <conditional name="application"> |
129 <param name="application_select" type="select" label="Condition"> | 186 <param name="application_select" type="select" label="Condition"> |
130 <option value="1">Apply to Every Point</option> | 187 <option value="1">Apply to Every Point</option> |
131 <option value="on">Check for presence/absence per chromosome</option> | 188 <option value="on">Check for presence/absence per chromosome</option> |
132 <option value="pos">Based on numerical position</option> | 189 <option value="pos">Based on numerical position</option> |
190 <option value="random">Randomly</option> | |
133 <option value="value">Apply based on point value</option> | 191 <option value="value">Apply based on point value</option> |
134 <option value="var">Apply based on GFF3 qualifier value (when available)</option> | 192 <option value="var">Apply based on qualifier value (when available)</option> |
135 </param> | 193 </param> |
136 <when value="1"> | 194 <when value="1"> |
137 </when> | 195 </when> |
138 <when value="on"> | 196 <when value="on"> |
139 <param name="on_genomes" type="text" label="Comma separated list of contig IDs"/> | 197 <param name="on_genomes" type="text" label="Comma separated list of contig IDs"/> |
140 </when> | 198 </when> |
141 <when value="pos"> | 199 <when value="pos"> |
142 <param name="pos_gt" type="float" label="Greater than this base" value="1000.0" help="Leave as zero to disable this test"/> | 200 <param name="pos_gt" type="float" label="Greater than this base" optional="true"/> |
143 <param name="pos_lt" type="float" label="Less than this base" value="0.0" help="Leave as zero to disable this test"/> | 201 <param name="pos_lt" type="float" label="Less than this base" optional="true"/> |
202 <param name="pos_lt_sub" type="boolean" truevalue="yes" falsevalue="no" label="Count 'Less than this base' from end of chromosome" /> | |
203 </when> | |
204 <when value="random"> | |
205 <param name="value" type="float" label="Percentage of bins" value="0.5" min="0" max="1" help="Randomly apply with this probability"/> | |
144 </when> | 206 </when> |
145 <when value="value"> | 207 <when value="value"> |
146 <param name="pos_gt" type="float" label="Points above this value" value="0.0" help="Leave as zero to disable this test"/> | 208 <param name="pos_gt" type="float" label="Points above this value" optional="true"/> |
147 <param name="pos_lt" type="float" label="Points below this value" value="0.0" help="Leave as zero to disable this test"/> | 209 <param name="pos_lt" type="float" label="Points below this value" optional="true"/> |
148 </when> | 210 </when> |
149 <when value="var"> | 211 <when value="var"> |
150 <param name="varname" type="text" label="Qualifier name" | 212 <param name="varname" type="text" label="Qualifier name" |
151 help="Set to the name of the qualifier in the GFF3 file you wish to compare against" /> | 213 help="Set to the name of the qualifier in the file you wish to compare against" /> |
152 | 214 |
153 <param name="cond_select" type="select" label="Condition"> | 215 <param name="cond_select" type="select" label="Condition"> |
154 <option value="eq">Equal to (string)</option> | 216 <option value="eq">Equal to (string)</option> |
217 <option value="==">Equal to (numeric)</option> | |
155 <option value="ne">Not equal to (string)</option> | 218 <option value="ne">Not equal to (string)</option> |
219 <option value="!=">Not equal to (numeric)</option> | |
220 <option value="<">Less than (numeric)</option> | |
221 <option value=">">Greater than (numeric)</option> | |
222 <option value="%">Modulus (numeric)</option> | |
223 <sanitizer> | |
224 <valid initial="string.letters"> | |
225 <add value=">" /> | |
226 <add value="<" /> | |
227 <add value="!" /> | |
228 <add value="=" /> | |
229 <add value="%" /> | |
230 </valid> | |
231 </sanitizer> | |
156 </param> | 232 </param> |
157 | 233 |
158 <param name="varvalue" type="text" label="Qualifier value to compare against"/> | 234 <param name="varvalue" type="text" label="Qualifier value to compare against"/> |
159 </when> | 235 </when> |
160 </conditional> | 236 </conditional> |
163 <conditional name="action"> | 239 <conditional name="action"> |
164 <param name="action_select" type="select" label="Action"> | 240 <param name="action_select" type="select" label="Action"> |
165 <option value="show">Change Visibility</option> | 241 <option value="show">Change Visibility</option> |
166 <option value="fill_color">Change Fill Color for all points</option> | 242 <option value="fill_color">Change Fill Color for all points</option> |
167 <option value="fill_color_value">Change Fill Color based on Value</option> | 243 <option value="fill_color_value">Change Fill Color based on Value</option> |
168 <option value="color">Change Stroke Color</option> | 244 <option value="stroke_color">Change Stroke Color</option> |
169 <option value="color_value">Change Stroke Color based on Value</option> | 245 <option value="color_value">Change Stroke Color based on Value</option> |
170 </param> | 246 </param> |
171 <when value="show"> | 247 <when value="show"> |
172 <param name="action_value" type="boolean" truevalue="yes" falsevalue="no" label="Show"/> | 248 <param name="action_value" type="boolean" truevalue="yes" falsevalue="no" label="Show"/> |
173 </when> | 249 </when> |
174 <when value="fill_color"> | 250 <when value="fill_color"> |
175 <expand macro="circos_color" name="action_value" label="Fill Color"/> | 251 <expand macro="circos_color" name="action_value" label="Fill Color"/> |
176 </when> | 252 </when> |
177 <when value="color"> | 253 <when value="stroke_color"> |
178 <expand macro="circos_color" name="action_value" label="Stroke Color"/> | 254 <expand macro="circos_color" name="action_value" label="Stroke Color"/> |
179 </when> | 255 </when> |
180 <when value="fill_color_value"> | 256 <when value="fill_color_value"> |
181 <expand macro="brewer_scale" name="action_value" label="Fill Color"/> | 257 <expand macro="brewer_scale" name="action_value" label="Fill Color"/> |
182 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> | 258 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> |
201 <section name="sec_link_rule" title="Rules"> | 277 <section name="sec_link_rule" title="Rules"> |
202 <repeat name="rules" title="Rule"> | 278 <repeat name="rules" title="Rule"> |
203 <repeat name="conditions" title="Conditions to Apply" help="Multiple conditions will be combined using AND"> | 279 <repeat name="conditions" title="Conditions to Apply" help="Multiple conditions will be combined using AND"> |
204 <conditional name="application"> | 280 <conditional name="application"> |
205 <param name="application_select" type="select" label="Condition"> | 281 <param name="application_select" type="select" label="Condition"> |
206 <option value="always">True / Always Applied</option> | 282 <option value="always" selected="true">True / Always Applied</option> |
283 <option value="random">Randomly</option> | |
207 <option value="interchr">Interchromosomal</option> | 284 <option value="interchr">Interchromosomal</option> |
208 <option value="intrachr">Intrachromosomal</option> | 285 <option value="intrachr">Intrachromosomal</option> |
209 <option value="chr">Chromosome</option> | 286 <option value="chr">Chromosome</option> |
210 <option value="dist">Distance between sides</option> | 287 <option value="dist">Distance between sides</option> |
211 <option value="start1">Start position Left</option> | 288 <option value="start1">Start position Left</option> |
254 <when value="rev2"/> | 331 <when value="rev2"/> |
255 <when value="inv"/> | 332 <when value="inv"/> |
256 <when value="interchr"/> | 333 <when value="interchr"/> |
257 <when value="intrachr"/> | 334 <when value="intrachr"/> |
258 <when value="always"/> | 335 <when value="always"/> |
336 <when value="random"> | |
337 <param name="value" type="float" label="Percentage" value="0.5" min="0" max="1" help="Randomly apply with this probability"/> | |
338 </when> | |
259 </conditional> | 339 </conditional> |
260 </repeat> | 340 </repeat> |
261 <repeat name="actions" title="Actions to Apply"> | 341 <repeat name="actions" title="Actions to Apply"> |
262 <conditional name="action"> | 342 <conditional name="action"> |
263 <param name="action_select" type="select" label="Action"> | 343 <param name="action_select" type="select" label="Action"> |
274 <param name="dynamic_select" type="select" label="Static / Dynamic Change"> | 354 <param name="dynamic_select" type="select" label="Static / Dynamic Change"> |
275 <option value="static">Static: Change is always applied</option> | 355 <option value="static">Static: Change is always applied</option> |
276 <option value="dynamic">Dynamic: Change is sometimes applied</option> | 356 <option value="dynamic">Dynamic: Change is sometimes applied</option> |
277 </param> | 357 </param> |
278 <when value="static"> | 358 <when value="static"> |
279 <expand macro="circos_color" label="Link Color" name="action_value"/> | 359 <expand macro="circos_color_alpha" label="Link Color" name="action_value"/> |
280 </when> | 360 </when> |
281 <when value="dynamic"> | 361 <when value="dynamic"> |
282 <expand macro="brewer_scale" label="Fill Color" name="action_value"/> | 362 <expand macro="brewer_scale" label="Fill Color" name="action_value"/> |
283 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> | 363 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/> |
284 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/> | 364 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/> |
337 <option value="fromto">from-to chromosome</option> | 417 <option value="fromto">from-to chromosome</option> |
338 <option value="between">between chromosomes</option> | 418 <option value="between">between chromosomes</option> |
339 </param> | 419 </param> |
340 <!-- TODO select chromosome from metadata/file column instead of text fields --> | 420 <!-- TODO select chromosome from metadata/file column instead of text fields --> |
341 <when value="on"> | 421 <when value="on"> |
342 <param name="compval" value="chr1" type="text" label="Chromosome"/> | 422 <param name="compval" value="chr1" type="text" label="Chromosome" help="Comma separated values are supported in this field"/> |
343 </when> | 423 </when> |
344 <when value="from"> | 424 <when value="from"> |
345 <param name="compval" value="chr1" type="text" label="Chromosome"/> | 425 <param name="compval" value="chr1" type="text" label="Chromosome"/> |
346 </when> | 426 </when> |
347 <when value="to"> | 427 <when value="to"> |