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comparison macros.xml @ 2:890ef899a3d7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:24 -0400
parents 95664f8de269
children a2b4b1b1a88e
comparison
equal deleted inserted replaced
1:95664f8de269 2:890ef899a3d7
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="&lt;">Less than (numeric)</option>
221 <option value="&gt;">Greater than (numeric)</option>
222 <option value="%">Modulus (numeric)</option>
223 <sanitizer>
224 <valid initial="string.letters">
225 <add value="&gt;" />
226 <add value="&lt;" />
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">