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comparison macros.xml @ 15:c7af51147b55 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068
author iuc
date Wed, 01 Oct 2025 19:34:28 +0000
parents d640aa8a24ab
children
comparison
equal deleted inserted replaced
14:d640aa8a24ab 15:c7af51147b55
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.8</token> 2 <token name="@TOOL_VERSION@">3.9</token>
3 <token name="@VERSION_SUFFIX@">2</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement>
7 <yield /> 7 <yield />
8 </requirements> 8 </requirements>
9 <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command> 9 <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>
10 </xml> 10 </xml>
11 11 <xml name="xrefs">
12 <xrefs>
13 <xref type="bio.tools">pygenometracks</xref>
14 </xrefs>
15 </xml>
12 <xml name="citations"> 16 <xml name="citations">
13 <citations> 17 <citations>
14 <citation type="doi">10.1038/s41467-017-02525-w</citation> 18 <citation type="doi">10.1038/s41467-017-02525-w</citation>
15 <citation type="doi">10.1093/bioinformatics/btaa692</citation> 19 <citation type="doi">10.1093/bioinformatics/btaa692</citation>
16 <yield /> 20 <yield />
38 label="Matricies to plot" multiple="true"/> 42 label="Matricies to plot" multiple="true"/>
39 </xml> 43 </xml>
40 <xml name="track_input_bed_macro"> 44 <xml name="track_input_bed_macro">
41 <param name="track_input_bed" type="data" format="bed" label="Track file(s) bed format" multiple="True"/> 45 <param name="track_input_bed" type="data" format="bed" label="Track file(s) bed format" multiple="True"/>
42 </xml> 46 </xml>
43 <xml name="track_input_bed_gtf_macro">
44 <param name="track_input_bed" type="data" format="bed,gtf" label="Track file(s) bed or gtf format" multiple="True"/>
45 </xml>
46 <xml name="track_input_narrow_peak_macro"> 47 <xml name="track_input_narrow_peak_macro">
47 <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file(s) encodepeak or bed format" multiple="True"/> 48 <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file(s) encodepeak or bed format" multiple="True"/>
48 </xml> 49 </xml>
49 <xml name="track_input_bed_single_macro"> 50 <xml name="track_input_bed_single_macro">
50 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/> 51 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>
205 <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false" 206 <param name="global_max_row" type="boolean" truevalue="true" falsevalue="false" checked="false"
206 label="Global max rows" /> 207 label="Global max rows" />
207 <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" /> 208 <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" />
208 <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" /> 209 <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" />
209 <param name="line_width" type="float" value="0.5" label="width of lines" /> 210 <param name="line_width" type="float" value="0.5" label="width of lines" />
210 <section name ="gtf" title="When using gtf as input" expanded="False"> 211 </xml>
211 <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label" 212 <xml name="height_utr_macro">
212 help="Usually transcript_name or gene_name"/>
213 <conditional name="merge_transcripts">
214 <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry">
215 <option value="false" selected="True">No</option>
216 <option value="true">Yes</option>
217 </param>
218 <when value="true">
219 <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true"
220 label="Merge overlapping exons" help="Usually it makes prettier plots" />
221 </when>
222 <when value="false" />
223 </conditional>
224 </section>
225 </xml>
226 <xml name="utr_macro">
227 <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/> 213 <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/>
214 </xml>
215 <xml name="color_utr_macro">
228 <conditional name="color_utr"> 216 <conditional name="color_utr">
229 <param name="color_utr_select" type="select" label="Define UTR color:"> 217 <param name="color_utr_select" type="select" label="Define UTR color:">
230 <option value="manually" selected="True">manually</option> 218 <option value="manually" selected="True">manually</option>
231 <option value="bed_rgb">From the 9th field</option> 219 <option value="bed_rgb">From the 9th field</option>
232 <option value="like">Like the coding</option> 220 <option value="like">Like the coding</option>
234 <when value="manually"> 222 <when value="manually">
235 <param name="color" type="color" value="grey" label="Color of UTR regions"/> 223 <param name="color" type="color" value="grey" label="Color of UTR regions"/>
236 </when> 224 </when>
237 <when value="bed_rgb" /> 225 <when value="bed_rgb" />
238 <when value="like" /> 226 <when value="like" />
227 </conditional>
228 </xml>
229 <xml name="bed_arrow_macro">
230 <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on exons"/>
231 <conditional name="color_arrow">
232 <param name="color_arrow_select" type="select" label="Define arrow color:">
233 <option value="manually" selected="True">manually</option>
234 <option value="bed_rgb">From the 9th field</option>
235 </param>
236 <when value="manually">
237 <param name="color" type="color" value="black" label="Color of arrows"/>
238 </when>
239 <when value="bed_rgb" />
240 </conditional>
241 </xml>
242 <xml name="bed_style_macro">
243 <conditional name="labels">
244 <param name="plot_labels" type="select" label="Plot labels">
245 <option value="true" selected="True">yes</option>
246 <option value="false">no</option>
247 </param>
248 <when value="true">
249 <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false"
250 label="Put all labels inside the plotted region"
251 help="Put labels on the left of the region if the region ends after the plotted region."/>
252 <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false"
253 label="Allow to put labels in the right margin"
254 help="Put labels in the margin if the region ends after the plotted region."/>
255 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
256 <param name="fontstyle" type="select" label="Fontstyle">
257 <option value="normal" selected="True">normal</option>
258 <option value="italic">italic</option>
259 <option value="oblique">oblique</option>
260 </param>
261 </when>
262 <when value="false"/>
263 </conditional>
264 <conditional name="bed_style">
265 <param name="bed_style_select" type="select" label="Bed style">
266 <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option>
267 <option value="UCSC">UCSC (blocks with arrows in introns)</option>
268 <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option>
269 <option value="exonarrows">exonarrows (large blocks with arrows in exons and smaller blocks for introns)</option>
270 </param>
271 <when value="flybase">
272 <expand macro="border_color_bed_macro" />
273 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
274 label="Include the arrowhead in the bed interval:"
275 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
276 <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
277 label="Size of arrowhead relative to the plotted region"
278 help="This size is also used to put space between the bed regions and their labels."/>
279 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
280 <expand macro="height_utr_macro" />
281 <expand macro="color_utr_macro" />
282 <expand macro="bed_advanced_macro" />
283 <expand macro="backbone_color_bed_macro" />
284 </section>
285 </when>
286 <when value="UCSC">
287 <expand macro="border_color_bed_macro" />
288 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
289 <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
290 label="Size of arrowhead relative to the plotted region"
291 help="This size is also used to put space between the bed regions and their labels."/>
292 <expand macro="bed_arrow_macro" />
293 <expand macro="bed_advanced_macro" />
294 <expand macro="backbone_color_bed_macro" />
295 </section>
296 </when>
297 <when value="tssarrow">
298 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
299 <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/>
300 <expand macro="height_utr_macro" />
301 <expand macro="color_utr_macro" />
302 <expand macro="bed_advanced_macro" />
303 <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
304 label="Size of arrowhead relative to the plotted region"
305 help="This size is also used to put space between the bed regions and their labels."/>
306 </section>
307 </when>
308 <when value="exonarrows">
309 <expand macro="border_color_bed_macro" />
310 <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
311 <expand macro="bed_arrow_macro" />
312 <param name="height_intron" type="float" value="0.5" min="0" max="1" label="relative height of introns compared to exons"/>
313 <expand macro="color_utr_macro" />
314 <expand macro="bed_advanced_macro" />
315 <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
316 label="Size of arrowhead relative to the plotted region"
317 help="This size is also used to put space between the bed regions and their labels."/>
318 </section>
319 </when>
320 </conditional>
321 </xml>
322 <xml name="delinv_labels">
323 <conditional name="labels">
324 <param name="plot_labels" type="select" label="Plot labels below">
325 <option value="true" selected="True">yes</option>
326 <option value="false">no</option>
327 </param>
328 <when value="true">
329 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
330 <param name="fontstyle" type="select" label="Fontstyle">
331 <option value="normal" selected="True">normal</option>
332 <option value="italic">italic</option>
333 <option value="oblique">oblique</option>
334 </param>
335 </when>
336 <when value="false"/>
239 </conditional> 337 </conditional>
240 </xml> 338 </xml>
241 <xml name="lines_macro"> 339 <xml name="lines_macro">
242 <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"/> 340 <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"/>
243 <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/> 341 <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/>