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comparison macros.xml @ 7:d691445a7d2e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
author iuc
date Fri, 17 Apr 2020 15:57:09 +0000
parents 0082bb149d37
children 345d24273a58
comparison
equal deleted inserted replaced
6:ad2e499da28f 7:d691445a7d2e
1 <macros> 1 <macros>
2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> 2 <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
3 <token name="@WRAPPER_VERSION@">3.2.1</token> 3 <token name="@WRAPPER_VERSION@">3.3</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement> 6 <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>
7 <yield /> 7 <yield />
8 </requirements> 8 </requirements>
13 <citations> 13 <citations>
14 <citation type="doi">10.5281/zenodo.1133705</citation> 14 <citation type="doi">10.5281/zenodo.1133705</citation>
15 <yield /> 15 <yield />
16 </citations> 16 </citations>
17 </xml> 17 </xml>
18
19 <xml name="colormap">
20 <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
21 <option value="RdYlBu">RdYlBu</option>
22 <option value="Accent">Accent</option>
23 <option value="Spectral">Spectral</option>
24 <option value="Set1">Set1</option>
25 <option value="Set2">Set2</option>
26 <option value="Set3">Set3</option>
27 <option value="Dark2">Dark2</option>
28 <option value="Reds">Reds</option>
29 <option value="Oranges">Oranges</option>
30 <option value="Greens">Greens</option>
31 <option value="Blues">Blues</option>
32 <option value="Greys">Greys</option>
33 <option value="Purples">Purples</option>
34 <option value="Paired">Paired</option>
35 <option value="Pastel1">Pastel1</option>
36 <option value="Pastel2">Pastel2</option>
37 <option value="spring">spring</option>
38 <option value="summer">summer</option>
39 <option value="autumn">autumn</option>
40 <option value="winter">winter</option>
41 <option value="hot">hot</option>
42 <option value="coolwarm">coolwarm</option>
43 <option value="cool">cool</option>
44 <option value="seismic">seismic</option>
45 <option value="terrain">terrain</option>
46 <option value="ocean">ocean</option>
47 <option value="rainbow">rainbow</option>
48 <option value="bone">bone</option>
49 <option value="flag">flag</option>
50 <option value="prism">prism</option>
51 <option value="cubehelix">cubehelix</option>
52 <option value="binary">binary</option>
53 <option value="pink">pink</option>
54 <option value="gray">gray</option>
55 <option value="copper">copper</option>
56 <option value="BrBG">BrBG</option>
57 <option value="BuGn">BuGn</option>
58 <option value="BuPu">BuPu</option>
59 <option value="GnBu">GnBu</option>
60 <option value="OrRd">OrRd</option>
61 <option value="PiYG">PiYG</option>
62 <option value="PRGn">PRGn</option>
63 <option value="PuOr">PuOr</option>
64 <option value="PuRd">PuRd</option>
65 <option value="PuBu">PuBu</option>
66 <option value="RdBu">RdBu</option>
67 <option value="RdGy">RdGy</option>
68 <option value="RdPu">RdPu</option>
69 <option value="YlGn">YlGn</option>
70 <option value="PuBuGn">PuBuGn</option>
71 <option value="RdYlGn">RdYlGn</option>
72 <option value="YlGnBu">YlGnBu</option>
73 <option value="YlOrBr">YlOrBr</option>
74 <option value="YlOrRd">YlOrRd</option>
75 <option value="gist_gray">gist_gray</option>
76 <option value="gist_stern">gist_stern</option>
77 <option value="gist_earth">gist_earth</option>
78 <option value="gist_yarg">gist_yarg</option>
79 <option value="gist_ncar">gist_ncar</option>
80 <option value="gist_rainbow">gist_rainbow</option>
81 <option value="gist_heat">gist_heat</option>
82 <option value="gnuplot">gnuplot</option>
83 <option value="gnuplot2">gnuplot2</option>
84 <option value="CMRmap">CMRmap</option>
85 <option value="bwr">bwr</option>
86 <option value="hsv">hsv</option>
87 <option value="brg">brg</option>
88 <option value="jet">jet</option>
89 <option value="afmhot">afmhot</option>
90 <option value="Accent_r">Accent reversed</option>
91 <option value="Spectral_r">Spectral reversed</option>
92 <option value="Set1_r">Set1 reversed</option>
93 <option value="Set2_r">Set2 reversed</option>
94 <option value="Set3_r">Set3 reversed</option>
95 <option value="Dark2_r">Dark2 reversed</option>
96 <option value="Reds_r">Reds reversed</option>
97 <option value="Oranges_r">Oranges reversed</option>
98 <option value="Greens_r">Greens reversed</option>
99 <option value="Blues_r">Blues reversed</option>
100 <option value="Greys_r">Greys reversed</option>
101 <option value="Purples_r">Purples reversed</option>
102 <option value="Paired_r">Paired reversed</option>
103 <option value="Pastel1_r">Pastel1 reversed</option>
104 <option value="Pastel2_r">Pastel2 reversed</option>
105 <option value="spring_r">spring reversed</option>
106 <option value="summer_r">summer reversed</option>
107 <option value="autumn_r">autumn reversed</option>
108 <option value="winter_r">winter reversed</option>
109 <option value="hot_r">hot reversed</option>
110 <option value="coolwarm_r">coolwarm reversed</option>
111 <option value="cool_r">cool reversed</option>
112 <option value="seismic_r">seismic reversed</option>
113 <option value="terrain_r">terrain reversed</option>
114 <option value="ocean_r">ocean reversed</option>
115 <option value="rainbow_r">rainbow reversed</option>
116 <option value="bone_r">bone reversed</option>
117 <option value="flag_r">flag reversed</option>
118 <option value="prism_r">prism reversed</option>
119 <option value="cubehelix_r">cubehelix reversed</option>
120 <option value="binary_r">binary reversed</option>
121 <option value="pink_r">pink reversed</option>
122 <option value="gray_r">gray reversed</option>
123 <option value="copper_r">copper reversed</option>
124 <option value="BrBG_r">BrBG reversed</option>
125 <option value="BuGn_r">BuGn reversed</option>
126 <option value="BuPu_r">BuPu reversed</option>
127 <option value="GnBu_r">GnBu reversed</option>
128 <option value="OrRd_r">OrRd reversed</option>
129 <option value="PiYG_r">PiYG reversed</option>
130 <option value="PRGn_r">PRGn reversed</option>
131 <option value="PuOr_r">PuOr reversed</option>
132 <option value="PuRd_r">PuRd reversed</option>
133 <option value="PuBu_r">PuBu reversed</option>
134 <option value="RdBu_r">RdBu reversed</option>
135 <option value="RdGy_r">RdGy reversed</option>
136 <option value="RdPu_r">RdPu reversed</option>
137 <option value="YlGn_r">YlGn reversed</option>
138 <option value="PuBuGn_r">PuBuGn reversed</option>
139 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
140 <option value="RdYlGn_r">RdYlGn reversed</option>
141 <option value="YlGnBu_r">YlGnBu reversed</option>
142 <option value="YlOrBr_r">YlOrBr reversed</option>
143 <option value="YlOrRd_r">YlOrRd reversed</option>
144 <option value="gist_gray_r">gist_gray reversed</option>
145 <option value="gist_stern_r">gist_stern reversed</option>
146 <option value="gist_earth_r">gist_earth reversed</option>
147 <option value="gist_yarg_r">gist_yarg reversed</option>
148 <option value="gist_ncar_r">gist_ncar reversed</option>
149 <option value="gist_rainbow_r">gist_rainbow reversed</option>
150 <option value="gist_heat_r">gist_heat reversed</option>
151 <option value="gnuplot_r">gnuplot reversed</option>
152 <option value="gnuplot2_r">gnuplot2 reversed</option>
153 <option value="CMRmap_r">CMRmap reversed</option>
154 <option value="bwr_r">bwr reversed</option>
155 <option value="hsv_r">hsv reversed</option>
156 <option value="brg_r">brg reversed</option>
157 <option value="jet_r">jet reversed</option>
158 <option value="afmhot_r">afmhot reversed</option>
159 </param>
160 </xml>
161
162 <xml name="region">
163 <param argument="--region" type="text" label="Region of the genome to limit the operation"
164 help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
165 </xml>
166
167 <xml name="matrix_h5_cooler_multiple_macro">
168 <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool"
169 label="Matricies to compute on" multiple="true"/>
170 </xml>
171 <token name="@REFERENCES@"> 18 <token name="@REFERENCES@">
172 19
173 .. class:: infomark 20 .. class:: infomark
174 21
175 For more information on the tools, please visit our `help site`_. 22 For more information on the tools, please visit our `help site`_.
182 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ 29 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
183 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de 30 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
184 .. _help site: https://github.com/deeptools/pyGenomeTracks 31 .. _help site: https://github.com/deeptools/pyGenomeTracks
185 32
186 </token> 33 </token>
187 34 <!-- all input files-->
35 <xml name="matrix_h5_cooler_multiple_macro">
36 <param name="matrix_h5_cooler_multiple" type="data" format="h5,cool"
37 label="Matricies to plot" multiple="true"/>
38 </xml>
188 <xml name="track_input_bed_macro"> 39 <xml name="track_input_bed_macro">
189 <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple="True"/> 40 <param name="track_input_bed" type="data" format="bed" label="Track file(s) bed format" multiple="True"/>
190 </xml> 41 </xml>
191 <xml name="track_input_bed_gtf_macro"> 42 <xml name="track_input_bed_gtf_macro">
192 <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple="True"/> 43 <param name="track_input_bed" type="data" format="bed,gtf" label="Track file(s) bed or gtf format" multiple="True"/>
193 </xml> 44 </xml>
194 <xml name="track_input_narrow_peak_macro"> 45 <xml name="track_input_narrow_peak_macro">
195 <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file encodepeak or format" multiple="True"/> 46 <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file(s) encodepeak or bed format" multiple="True"/>
196 </xml> 47 </xml>
197 <xml name="track_input_bed_single_macro"> 48 <xml name="track_input_bed_single_macro">
198 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/> 49 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>
199 </xml> 50 </xml>
200 <xml name="track_input_bedgraph_macro"> 51 <xml name="track_input_bedgraph_macro">
201 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple="True"/> 52 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/>
202 </xml> 53 </xml>
203 <xml name="track_input_bigwig_macro"> 54 <xml name="track_input_bigwig_macro">
204 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file bigwig format" multiple="True"/> 55 <param name="track_input_bigwig" type="data" format="bigwig" label="Track file(s) bigwig format" multiple="True"/>
205 </xml> 56 </xml>
206 <xml name="track_input_bedgraph_matrix_macro"> 57 <xml name="track_input_bedgraph_matrix_macro">
207 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file bigwig format" multiple="True"/> 58 <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/>
208 </xml> 59 </xml>
209 <xml name="track_input_link_macro"> 60 <xml name="track_input_link_macro">
210 <param name="track_input_link" type="data" format="bed,interval" label="Track file for links" multiple="False"/> 61 <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/>
211 </xml> 62 </xml>
63 <!-- Common to nearly all tracks: -->
212 <xml name="plot_title"> 64 <xml name="plot_title">
213 <param name="title" type="text" optional="true" label="Plot title" multiple="True"/> 65 <param name="title" type="text" optional="true" label="Plot title" multiple="True"/>
214 </xml> 66 </xml>
215 <xml name="spacer_macro"> 67 <xml name="spacer_macro">
216 <param name="spacer_height" type="float" value="" optional="True" 68 <param name="spacer_height" type="float" value="" optional="True"
218 </xml> 70 </xml>
219 <xml name="inverted_macro"> 71 <xml name="inverted_macro">
220 <param name="invert_orientation" type="boolean" truevalue="true" falsevalue="false" checked="false" 72 <param name="invert_orientation" type="boolean" truevalue="true" falsevalue="false" checked="false"
221 label="Invert the track" /> 73 label="Invert the track" />
222 </xml> 74 </xml>
223 <xml name="color_bed_macro"> 75 <xml name="overlay_macro">
224 <conditional name="color_bed"> 76 <param name="overlay_select" type="select" label="Overlay this track with the previous one:">
225 <param name="color_bed_select" type="select" label="Use color:"> 77 <option value="no" selected="True">No</option>
226 <option value="manually" selected="True">manually</option> 78 <option value="yes">Yes</option>
227 <option value="bed_rgb">From the 9th field</option> 79 <option value="share-y">Yes and keep same y axis</option>
228 <option value="colormap">From the 5th field (score)</option> 80 </param>
229 </param> 81 </xml>
230 <when value="manually"> 82 <xml name="minmax_macro">
231 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 83 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
232 </when> 84 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
233 <when value="bed_rgb" /> 85 </xml>
234 <when value="colormap"> 86 <!-- More specific but still present twice:-->
235 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
236 <option value="RdYlBu">RdYlBu</option>
237 <option value="Accent">Accent</option>
238 <option value="Spectral">Spectral</option>
239 <option value="Set1">Set1</option>
240 <option value="Set2">Set2</option>
241 <option value="Set3">Set3</option>
242 <option value="Dark2">Dark2</option>
243 <option value="Reds">Reds</option>
244 <option value="Oranges">Oranges</option>
245 <option value="Greens">Greens</option>
246 <option value="Blues">Blues</option>
247 <option value="Greys">Greys</option>
248 <option value="Purples">Purples</option>
249 <option value="Paired">Paired</option>
250 <option value="Pastel1">Pastel1</option>
251 <option value="Pastel2">Pastel2</option>
252 <option value="spring">spring</option>
253 <option value="summer">summer</option>
254 <option value="autumn">autumn</option>
255 <option value="winter">winter</option>
256 <option value="hot">hot</option>
257 <option value="coolwarm">coolwarm</option>
258 <option value="cool">cool</option>
259 <option value="seismic">seismic</option>
260 <option value="terrain">terrain</option>
261 <option value="ocean">ocean</option>
262 <option value="rainbow">rainbow</option>
263 <option value="bone">bone</option>
264 <option value="flag">flag</option>
265 <option value="prism">prism</option>
266 <option value="cubehelix">cubehelix</option>
267 <option value="binary">binary</option>
268 <option value="pink">pink</option>
269 <option value="gray">gray</option>
270 <option value="copper">copper</option>
271 <option value="BrBG">BrBG</option>
272 <option value="BuGn">BuGn</option>
273 <option value="BuPu">BuPu</option>
274 <option value="GnBu">GnBu</option>
275 <option value="OrRd">OrRd</option>
276 <option value="PiYG">PiYG</option>
277 <option value="PRGn">PRGn</option>
278 <option value="PuOr">PuOr</option>
279 <option value="PuRd">PuRd</option>
280 <option value="PuBu">PuBu</option>
281 <option value="RdBu">RdBu</option>
282 <option value="RdGy">RdGy</option>
283 <option value="RdPu">RdPu</option>
284 <option value="YlGn">YlGn</option>
285 <option value="PuBuGn">PuBuGn</option>
286 <option value="RdYlGn">RdYlGn</option>
287 <option value="YlGnBu">YlGnBu</option>
288 <option value="YlOrBr">YlOrBr</option>
289 <option value="YlOrRd">YlOrRd</option>
290 <option value="gist_gray">gist_gray</option>
291 <option value="gist_stern">gist_stern</option>
292 <option value="gist_earth">gist_earth</option>
293 <option value="gist_yarg">gist_yarg</option>
294 <option value="gist_ncar">gist_ncar</option>
295 <option value="gist_rainbow">gist_rainbow</option>
296 <option value="gist_heat">gist_heat</option>
297 <option value="gnuplot">gnuplot</option>
298 <option value="gnuplot2">gnuplot2</option>
299 <option value="CMRmap">CMRmap</option>
300 <option value="bwr">bwr</option>
301 <option value="hsv">hsv</option>
302 <option value="brg">brg</option>
303 <option value="jet">jet</option>
304 <option value="afmhot">afmhot</option>
305 <option value="Accent_r">Accent reversed</option>
306 <option value="Spectral_r">Spectral reversed</option>
307 <option value="Set1_r">Set1 reversed</option>
308 <option value="Set2_r">Set2 reversed</option>
309 <option value="Set3_r">Set3 reversed</option>
310 <option value="Dark2_r">Dark2 reversed</option>
311 <option value="Reds_r">Reds reversed</option>
312 <option value="Oranges_r">Oranges reversed</option>
313 <option value="Greens_r">Greens reversed</option>
314 <option value="Blues_r">Blues reversed</option>
315 <option value="Greys_r">Greys reversed</option>
316 <option value="Purples_r">Purples reversed</option>
317 <option value="Paired_r">Paired reversed</option>
318 <option value="Pastel1_r">Pastel1 reversed</option>
319 <option value="Pastel2_r">Pastel2 reversed</option>
320 <option value="spring_r">spring reversed</option>
321 <option value="summer_r">summer reversed</option>
322 <option value="autumn_r">autumn reversed</option>
323 <option value="winter_r">winter reversed</option>
324 <option value="hot_r">hot reversed</option>
325 <option value="coolwarm_r">coolwarm reversed</option>
326 <option value="cool_r">cool reversed</option>
327 <option value="seismic_r">seismic reversed</option>
328 <option value="terrain_r">terrain reversed</option>
329 <option value="ocean_r">ocean reversed</option>
330 <option value="rainbow_r">rainbow reversed</option>
331 <option value="bone_r">bone reversed</option>
332 <option value="flag_r">flag reversed</option>
333 <option value="prism_r">prism reversed</option>
334 <option value="cubehelix_r">cubehelix reversed</option>
335 <option value="binary_r">binary reversed</option>
336 <option value="pink_r">pink reversed</option>
337 <option value="gray_r">gray reversed</option>
338 <option value="copper_r">copper reversed</option>
339 <option value="BrBG_r">BrBG reversed</option>
340 <option value="BuGn_r">BuGn reversed</option>
341 <option value="BuPu_r">BuPu reversed</option>
342 <option value="GnBu_r">GnBu reversed</option>
343 <option value="OrRd_r">OrRd reversed</option>
344 <option value="PiYG_r">PiYG reversed</option>
345 <option value="PRGn_r">PRGn reversed</option>
346 <option value="PuOr_r">PuOr reversed</option>
347 <option value="PuRd_r">PuRd reversed</option>
348 <option value="PuBu_r">PuBu reversed</option>
349 <option value="RdBu_r">RdBu reversed</option>
350 <option value="RdGy_r">RdGy reversed</option>
351 <option value="RdPu_r">RdPu reversed</option>
352 <option value="YlGn_r">YlGn reversed</option>
353 <option value="PuBuGn_r">PuBuGn reversed</option>
354 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
355 <option value="RdYlGn_r">RdYlGn reversed</option>
356 <option value="YlGnBu_r">YlGnBu reversed</option>
357 <option value="YlOrBr_r">YlOrBr reversed</option>
358 <option value="YlOrRd_r">YlOrRd reversed</option>
359 <option value="gist_gray_r">gist_gray reversed</option>
360 <option value="gist_stern_r">gist_stern reversed</option>
361 <option value="gist_earth_r">gist_earth reversed</option>
362 <option value="gist_yarg_r">gist_yarg reversed</option>
363 <option value="gist_ncar_r">gist_ncar reversed</option>
364 <option value="gist_rainbow_r">gist_rainbow reversed</option>
365 <option value="gist_heat_r">gist_heat reversed</option>
366 <option value="gnuplot_r">gnuplot reversed</option>
367 <option value="gnuplot2_r">gnuplot2 reversed</option>
368 <option value="CMRmap_r">CMRmap reversed</option>
369 <option value="bwr_r">bwr reversed</option>
370 <option value="hsv_r">hsv reversed</option>
371 <option value="brg_r">brg reversed</option>
372 <option value="jet_r">jet reversed</option>
373 <option value="afmhot_r">afmhot reversed</option>
374 </param>
375 </when>
376 </conditional>
377 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
378 </xml>
379 <xml name="color_coverage_macro"> 87 <xml name="color_coverage_macro">
380 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 88 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
381 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> 89 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
382 <conditional name="color_negative"> 90 <conditional name="color_negative">
383 <param name="color_negative_select" type="select" label="Use a different color for negative values"> 91 <param name="color_negative_select" type="select" label="Use a different color for negative values">
388 <when value="true"> 96 <when value="true">
389 <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" /> 97 <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" />
390 </when> 98 </when>
391 </conditional> 99 </conditional>
392 </xml> 100 </xml>
393 <xml name="overlay_macro">
394 <param name="overlay_select" type="select" label="Overlay this track with the previous one:">
395 <option value="no" selected="True">No</option>
396 <option value="yes">Yes</option>
397 <option value="share-y">Yes and keep same y axis</option>
398 </param>
399 </xml>
400 <xml name="type_coverage_macro"> 101 <xml name="type_coverage_macro">
401 <conditional name="type_conditional"> 102 <conditional name="type_conditional">
402 <param name="type_selector" type="select" label="Choose style of the plot."> 103 <param name="type_selector" type="select" label="Choose style of the plot.">
403 <option value="fill_option">fill</option> 104 <option value="fill_option">fill</option>
404 <option value="line_option">line</option> 105 <option value="line_option">line</option>
411 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/> 112 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
412 </when> 113 </when>
413 <when value="fill_option" /> 114 <when value="fill_option" />
414 </conditional> 115 </conditional>
415 </xml> 116 </xml>
416 <xml name="minmax_macro"> 117 <xml name="border_color_bed_macro">
417 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 118 <conditional name="border_color_bed">
418 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> 119 <param name="border_color_bed_select" type="select" label="Define border color:">
419 </xml> 120 <option value="manually" selected="True">manually</option>
420 <xml name="reading_bw_macro"> 121 <option value="bed_rgb">From the 9th field</option>
421 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False"> 122 <option value="none">No border</option>
422 <param name="summary" type="select" label="Summary method">
423 <option value="mean" selected="True">mean=mean value</option>
424 <option value="min">min=minimum value</option>
425 <option value="max">max=maximum value</option>
426 <option value="coverage">coverage=number of covered bases</option>
427 <option value="std">std=standard deviation</option>
428 </param> 123 </param>
429 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> 124 <when value="manually">
430 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" 125 <param name="color" type="color" value="#000000" label="Color of the border"/>
431 label="NAN's to zeros" /> 126 </when>
127 <when value="bed_rgb" />
128 <when value="none" />
129 </conditional>
130 </xml>
131 <xml name="bed_advanced_macro">
132 <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false"
133 label="Global max rows" />
134 <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" />
135 <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" />
136 <param name="line_width" type="float" value="0.5" label="width of lines" />
137 <section name ="gtf" title="When using gtf as input" expanded="False">
138 <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
139 help="Usually transcript_name or gene_name"/>
140 <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false"
141 label="Merge all transcripts of each gene in a single entry" />
432 </section> 142 </section>
433 </xml> 143 </xml>
434 <xml name="bed_advanced_macro"> 144 <xml name="utr_macro">
435 <section name="bed_advanced" title="Configure other bed parameters" expanded="False"> 145 <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/>
436 <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false" 146 <conditional name="color_utr">
437 label="Global max rows" /> 147 <param name="color_utr_select" type="select" label="Define UTR color:">
438 <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" /> 148 <option value="manually" selected="True">manually</option>
439 <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" /> 149 <option value="bed_rgb">From the 9th field</option>
440 <param name="line_width" type="float" value="0.5" label="width of lines" /> 150 <option value="like">Like the coding</option>
441 <section name ="flybase" title="When using flybase style" expanded="False"> 151 </param>
442 <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions in flybase style"/> 152 <when value="manually">
443 <param name="color_utr" type="color" value="grey" label="Color of UTR regions"/> 153 <param name="color" type="color" value="grey" label="Color of UTR regions"/>
444 </section> 154 </when>
445 <section name ="ucsc" title="When using UCSC style" expanded="False"> 155 <when value="bed_rgb" />
446 <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on introns in UCSC style"/> 156 <when value="like" />
447 </section> 157 </conditional>
448 <section name ="gtf" title="When using gtf as input" expanded="False">
449 <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
450 help="Usually transcript_name or gene_name"/>
451 <param name="merge_transcripts" type="boolean" truevalue="true" falsevalue="false" checked="false"
452 label="Merge all transcripts of each gene in a single entry" />
453 </section>
454 </section>
455 </xml> 158 </xml>
456 <xml name="lines_macro"> 159 <xml name="lines_macro">
457 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/> 160 <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
458 <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/> 161 <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/>
459 <param name="line_style" type="select" label="Style of the line(s)"> 162 <param name="line_style" type="select" label="Style of the line(s)">
461 <option value="dashed">Dashed</option> 164 <option value="dashed">Dashed</option>
462 <option value="dotted">Dotted</option> 165 <option value="dotted">Dotted</option>
463 <option value="dashdot">Dashdot</option> 166 <option value="dashdot">Dashdot</option>
464 </param> 167 </param>
465 </xml> 168 </xml>
466 <xml name="links_color_macro"> 169 <xml name="colormap_macro">
467 <conditional name="color_link"> 170 <option value="RdYlBu">RdYlBu</option>
468 <param name="color_link_select" type="select" label="Use color:"> 171 <option value="Accent">Accent</option>
469 <option value="manually" selected="True">manually</option> 172 <option value="Spectral">Spectral</option>
470 <option value="colormap">From the 7th field (score)</option> 173 <option value="Set1">Set1</option>
471 </param> 174 <option value="Set2">Set2</option>
472 <when value="manually"> 175 <option value="Set3">Set3</option>
473 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 176 <option value="Dark2">Dark2</option>
474 </when> 177 <option value="Reds">Reds</option>
475 <when value="colormap"> 178 <option value="Oranges">Oranges</option>
476 <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> 179 <option value="Greens">Greens</option>
477 <option value="RdYlBu">RdYlBu</option> 180 <option value="Blues">Blues</option>
478 <option value="Accent">Accent</option> 181 <option value="Greys">Greys</option>
479 <option value="Spectral">Spectral</option> 182 <option value="Purples">Purples</option>
480 <option value="Set1">Set1</option> 183 <option value="Paired">Paired</option>
481 <option value="Set2">Set2</option> 184 <option value="Pastel1">Pastel1</option>
482 <option value="Set3">Set3</option> 185 <option value="Pastel2">Pastel2</option>
483 <option value="Dark2">Dark2</option> 186 <option value="spring">spring</option>
484 <option value="Reds">Reds</option> 187 <option value="summer">summer</option>
485 <option value="Oranges">Oranges</option> 188 <option value="autumn">autumn</option>
486 <option value="Greens">Greens</option> 189 <option value="winter">winter</option>
487 <option value="Blues">Blues</option> 190 <option value="hot">hot</option>
488 <option value="Greys">Greys</option> 191 <option value="coolwarm">coolwarm</option>
489 <option value="Purples">Purples</option> 192 <option value="cool">cool</option>
490 <option value="Paired">Paired</option> 193 <option value="seismic">seismic</option>
491 <option value="Pastel1">Pastel1</option> 194 <option value="terrain">terrain</option>
492 <option value="Pastel2">Pastel2</option> 195 <option value="ocean">ocean</option>
493 <option value="spring">spring</option> 196 <option value="rainbow">rainbow</option>
494 <option value="summer">summer</option> 197 <option value="bone">bone</option>
495 <option value="autumn">autumn</option> 198 <option value="flag">flag</option>
496 <option value="winter">winter</option> 199 <option value="prism">prism</option>
497 <option value="hot">hot</option> 200 <option value="cubehelix">cubehelix</option>
498 <option value="coolwarm">coolwarm</option> 201 <option value="binary">binary</option>
499 <option value="cool">cool</option> 202 <option value="pink">pink</option>
500 <option value="seismic">seismic</option> 203 <option value="gray">gray</option>
501 <option value="terrain">terrain</option> 204 <option value="copper">copper</option>
502 <option value="ocean">ocean</option> 205 <option value="BrBG">BrBG</option>
503 <option value="rainbow">rainbow</option> 206 <option value="BuGn">BuGn</option>
504 <option value="bone">bone</option> 207 <option value="BuPu">BuPu</option>
505 <option value="flag">flag</option> 208 <option value="GnBu">GnBu</option>
506 <option value="prism">prism</option> 209 <option value="OrRd">OrRd</option>
507 <option value="cubehelix">cubehelix</option> 210 <option value="PiYG">PiYG</option>
508 <option value="binary">binary</option> 211 <option value="PRGn">PRGn</option>
509 <option value="pink">pink</option> 212 <option value="PuOr">PuOr</option>
510 <option value="gray">gray</option> 213 <option value="PuRd">PuRd</option>
511 <option value="copper">copper</option> 214 <option value="PuBu">PuBu</option>
512 <option value="BrBG">BrBG</option> 215 <option value="RdBu">RdBu</option>
513 <option value="BuGn">BuGn</option> 216 <option value="RdGy">RdGy</option>
514 <option value="BuPu">BuPu</option> 217 <option value="RdPu">RdPu</option>
515 <option value="GnBu">GnBu</option> 218 <option value="YlGn">YlGn</option>
516 <option value="OrRd">OrRd</option> 219 <option value="PuBuGn">PuBuGn</option>
517 <option value="PiYG">PiYG</option> 220 <option value="RdYlGn">RdYlGn</option>
518 <option value="PRGn">PRGn</option> 221 <option value="YlGnBu">YlGnBu</option>
519 <option value="PuOr">PuOr</option> 222 <option value="YlOrBr">YlOrBr</option>
520 <option value="PuRd">PuRd</option> 223 <option value="YlOrRd">YlOrRd</option>
521 <option value="PuBu">PuBu</option> 224 <option value="gist_gray">gist_gray</option>
522 <option value="RdBu">RdBu</option> 225 <option value="gist_stern">gist_stern</option>
523 <option value="RdGy">RdGy</option> 226 <option value="gist_earth">gist_earth</option>
524 <option value="RdPu">RdPu</option> 227 <option value="gist_yarg">gist_yarg</option>
525 <option value="YlGn">YlGn</option> 228 <option value="gist_ncar">gist_ncar</option>
526 <option value="PuBuGn">PuBuGn</option> 229 <option value="gist_rainbow">gist_rainbow</option>
527 <option value="RdYlGn">RdYlGn</option> 230 <option value="gist_heat">gist_heat</option>
528 <option value="YlGnBu">YlGnBu</option> 231 <option value="gnuplot">gnuplot</option>
529 <option value="YlOrBr">YlOrBr</option> 232 <option value="gnuplot2">gnuplot2</option>
530 <option value="YlOrRd">YlOrRd</option> 233 <option value="CMRmap">CMRmap</option>
531 <option value="gist_gray">gist_gray</option> 234 <option value="bwr">bwr</option>
532 <option value="gist_stern">gist_stern</option> 235 <option value="hsv">hsv</option>
533 <option value="gist_earth">gist_earth</option> 236 <option value="brg">brg</option>
534 <option value="gist_yarg">gist_yarg</option> 237 <option value="jet">jet</option>
535 <option value="gist_ncar">gist_ncar</option> 238 <option value="afmhot">afmhot</option>
536 <option value="gist_rainbow">gist_rainbow</option> 239 <option value="viridis">viridis</option>
537 <option value="gist_heat">gist_heat</option> 240 <option value="plasma">plasma</option>
538 <option value="gnuplot">gnuplot</option> 241 <option value="inferno">inferno</option>
539 <option value="gnuplot2">gnuplot2</option> 242 <option value="magma">magma</option>
540 <option value="CMRmap">CMRmap</option> 243 <option value="cividis">cividis</option>
541 <option value="bwr">bwr</option> 244 <option value="Accent_r">Accent reversed</option>
542 <option value="hsv">hsv</option> 245 <option value="Spectral_r">Spectral reversed</option>
543 <option value="brg">brg</option> 246 <option value="Set1_r">Set1 reversed</option>
544 <option value="jet">jet</option> 247 <option value="Set2_r">Set2 reversed</option>
545 <option value="afmhot">afmhot</option> 248 <option value="Set3_r">Set3 reversed</option>
546 <option value="Accent_r">Accent reversed</option> 249 <option value="Dark2_r">Dark2 reversed</option>
547 <option value="Spectral_r">Spectral reversed</option> 250 <option value="Reds_r">Reds reversed</option>
548 <option value="Set1_r">Set1 reversed</option> 251 <option value="Oranges_r">Oranges reversed</option>
549 <option value="Set2_r">Set2 reversed</option> 252 <option value="Greens_r">Greens reversed</option>
550 <option value="Set3_r">Set3 reversed</option> 253 <option value="Blues_r">Blues reversed</option>
551 <option value="Dark2_r">Dark2 reversed</option> 254 <option value="Greys_r">Greys reversed</option>
552 <option value="Reds_r">Reds reversed</option> 255 <option value="Purples_r">Purples reversed</option>
553 <option value="Oranges_r">Oranges reversed</option> 256 <option value="Paired_r">Paired reversed</option>
554 <option value="Greens_r">Greens reversed</option> 257 <option value="Pastel1_r">Pastel1 reversed</option>
555 <option value="Blues_r">Blues reversed</option> 258 <option value="Pastel2_r">Pastel2 reversed</option>
556 <option value="Greys_r">Greys reversed</option> 259 <option value="spring_r">spring reversed</option>
557 <option value="Purples_r">Purples reversed</option> 260 <option value="summer_r">summer reversed</option>
558 <option value="Paired_r">Paired reversed</option> 261 <option value="autumn_r">autumn reversed</option>
559 <option value="Pastel1_r">Pastel1 reversed</option> 262 <option value="winter_r">winter reversed</option>
560 <option value="Pastel2_r">Pastel2 reversed</option> 263 <option value="hot_r">hot reversed</option>
561 <option value="spring_r">spring reversed</option> 264 <option value="coolwarm_r">coolwarm reversed</option>
562 <option value="summer_r">summer reversed</option> 265 <option value="cool_r">cool reversed</option>
563 <option value="autumn_r">autumn reversed</option> 266 <option value="seismic_r">seismic reversed</option>
564 <option value="winter_r">winter reversed</option> 267 <option value="terrain_r">terrain reversed</option>
565 <option value="hot_r">hot reversed</option> 268 <option value="ocean_r">ocean reversed</option>
566 <option value="coolwarm_r">coolwarm reversed</option> 269 <option value="rainbow_r">rainbow reversed</option>
567 <option value="cool_r">cool reversed</option> 270 <option value="bone_r">bone reversed</option>
568 <option value="seismic_r">seismic reversed</option> 271 <option value="flag_r">flag reversed</option>
569 <option value="terrain_r">terrain reversed</option> 272 <option value="prism_r">prism reversed</option>
570 <option value="ocean_r">ocean reversed</option> 273 <option value="cubehelix_r">cubehelix reversed</option>
571 <option value="rainbow_r">rainbow reversed</option> 274 <option value="binary_r">binary reversed</option>
572 <option value="bone_r">bone reversed</option> 275 <option value="pink_r">pink reversed</option>
573 <option value="flag_r">flag reversed</option> 276 <option value="gray_r">gray reversed</option>
574 <option value="prism_r">prism reversed</option> 277 <option value="copper_r">copper reversed</option>
575 <option value="cubehelix_r">cubehelix reversed</option> 278 <option value="BrBG_r">BrBG reversed</option>
576 <option value="binary_r">binary reversed</option> 279 <option value="BuGn_r">BuGn reversed</option>
577 <option value="pink_r">pink reversed</option> 280 <option value="BuPu_r">BuPu reversed</option>
578 <option value="gray_r">gray reversed</option> 281 <option value="GnBu_r">GnBu reversed</option>
579 <option value="copper_r">copper reversed</option> 282 <option value="OrRd_r">OrRd reversed</option>
580 <option value="BrBG_r">BrBG reversed</option> 283 <option value="PiYG_r">PiYG reversed</option>
581 <option value="BuGn_r">BuGn reversed</option> 284 <option value="PRGn_r">PRGn reversed</option>
582 <option value="BuPu_r">BuPu reversed</option> 285 <option value="PuOr_r">PuOr reversed</option>
583 <option value="GnBu_r">GnBu reversed</option> 286 <option value="PuRd_r">PuRd reversed</option>
584 <option value="OrRd_r">OrRd reversed</option> 287 <option value="PuBu_r">PuBu reversed</option>
585 <option value="PiYG_r">PiYG reversed</option> 288 <option value="RdBu_r">RdBu reversed</option>
586 <option value="PRGn_r">PRGn reversed</option> 289 <option value="RdGy_r">RdGy reversed</option>
587 <option value="PuOr_r">PuOr reversed</option> 290 <option value="RdPu_r">RdPu reversed</option>
588 <option value="PuRd_r">PuRd reversed</option> 291 <option value="YlGn_r">YlGn reversed</option>
589 <option value="PuBu_r">PuBu reversed</option> 292 <option value="PuBuGn_r">PuBuGn reversed</option>
590 <option value="RdBu_r">RdBu reversed</option> 293 <option value="RdYlBu_r">RdYlBu reversed</option>
591 <option value="RdGy_r">RdGy reversed</option> 294 <option value="RdYlGn_r">RdYlGn reversed</option>
592 <option value="RdPu_r">RdPu reversed</option> 295 <option value="YlGnBu_r">YlGnBu reversed</option>
593 <option value="YlGn_r">YlGn reversed</option> 296 <option value="YlOrBr_r">YlOrBr reversed</option>
594 <option value="PuBuGn_r">PuBuGn reversed</option> 297 <option value="YlOrRd_r">YlOrRd reversed</option>
595 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option> 298 <option value="gist_gray_r">gist_gray reversed</option>
596 <option value="RdYlGn_r">RdYlGn reversed</option> 299 <option value="gist_stern_r">gist_stern reversed</option>
597 <option value="YlGnBu_r">YlGnBu reversed</option> 300 <option value="gist_earth_r">gist_earth reversed</option>
598 <option value="YlOrBr_r">YlOrBr reversed</option> 301 <option value="gist_yarg_r">gist_yarg reversed</option>
599 <option value="YlOrRd_r">YlOrRd reversed</option> 302 <option value="gist_ncar_r">gist_ncar reversed</option>
600 <option value="gist_gray_r">gist_gray reversed</option> 303 <option value="gist_rainbow_r">gist_rainbow reversed</option>
601 <option value="gist_stern_r">gist_stern reversed</option> 304 <option value="gist_heat_r">gist_heat reversed</option>
602 <option value="gist_earth_r">gist_earth reversed</option> 305 <option value="gnuplot_r">gnuplot reversed</option>
603 <option value="gist_yarg_r">gist_yarg reversed</option> 306 <option value="gnuplot2_r">gnuplot2 reversed</option>
604 <option value="gist_ncar_r">gist_ncar reversed</option> 307 <option value="CMRmap_r">CMRmap reversed</option>
605 <option value="gist_rainbow_r">gist_rainbow reversed</option> 308 <option value="bwr_r">bwr reversed</option>
606 <option value="gist_heat_r">gist_heat reversed</option> 309 <option value="hsv_r">hsv reversed</option>
607 <option value="gnuplot_r">gnuplot reversed</option> 310 <option value="brg_r">brg reversed</option>
608 <option value="gnuplot2_r">gnuplot2 reversed</option> 311 <option value="jet_r">jet reversed</option>
609 <option value="CMRmap_r">CMRmap reversed</option> 312 <option value="afmhot_r">afmhot reversed</option>
610 <option value="bwr_r">bwr reversed</option> 313 <option value="viridis_r">viridis reversed</option>
611 <option value="hsv_r">hsv reversed</option> 314 <option value="plasma_r">plasma reversed</option>
612 <option value="brg_r">brg reversed</option> 315 <option value="inferno_r">inferno reversed</option>
613 <option value="jet_r">jet reversed</option> 316 <option value="magma_r">magma reversed</option>
614 <option value="afmhot_r">afmhot reversed</option> 317 <option value="cividis_r">cividis reversed</option>
615 </param>
616 </when>
617 </conditional>
618 </xml> 318 </xml>
619 </macros> 319 </macros>