Mercurial > repos > iuc > pygenometracks

comparison macros.xml @ 2:c171f2b7d76e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
author iuc
date Fri, 23 Aug 2019 07:24:20 -0400
parents 2074627b0f83
children c237ba772225
comparison
equal deleted inserted replaced
1:0ea86f6bf2a1 2:c171f2b7d76e
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@">2.0</token> 3 <token name="@WRAPPER_VERSION@">3.1</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 <!--<requirement type="package" version="3.7">python</requirement>-->
7 <yield /> 8 <yield />
8 </requirements> 9 </requirements>
9 <version_command>@BINARY@ --version</version_command> 10 <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>
10 </xml> 11 </xml>
11 12
12 <xml name="citations"> 13 <xml name="citations">
13 <citations> 14 <citations>
14 <citation type="doi">10.5281/zenodo.1133705</citation> 15 <citation type="doi">10.5281/zenodo.1133705</citation>
186 </token> 187 </token>
187 188
188 <xml name="track_input_bed_macro"> 189 <xml name="track_input_bed_macro">
189 <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple='True'/> 190 <param name="track_input_bed" type="data" format="bed" label="Track file bed format" multiple='True'/>
190 </xml> 191 </xml>
192 <xml name="track_input_bed_gtf_macro">
193 <param name="track_input_bed" type="data" format="bed,gtf" label="Track file bed or gtf format" multiple='True'/>
194 </xml>
191 <xml name="track_input_bed_single_macro"> 195 <xml name="track_input_bed_single_macro">
192 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/> 196 <param name="track_input_bed_single" type="data" format="bed" label="Track file bed format"/>
193 </xml> 197 </xml>
194 <xml name="track_input_bedgraph_macro"> 198 <xml name="track_input_bedgraph_macro">
195 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple='True'/> 199 <param name="track_input_bedgraph" type="data" format="bedgraph" label="Track file bedgraph format" multiple='True'/>
205 </xml> 209 </xml>
206 <xml name="spacer_macro"> 210 <xml name="spacer_macro">
207 <param name="spacer_height" type="float" value="" optional="True" 211 <param name="spacer_height" type="float" value="" optional="True"
208 label="Include spacer at the end of the track" help="Height of the spacer." /> 212 label="Include spacer at the end of the track" help="Height of the spacer." />
209 </xml> 213 </xml>
214 <xml name="inverted_macro">
215 <param name="invert_orientation" type="boolean" truevalue="yes" falsevalue="no" checked="false"
216 label="Invert the track" />
217 </xml>
218 <xml name="color_bed_macro">
219 <conditional name="color_bed">
220 <param name="color_bed_select" type="select" label="Use color:">
221 <option value="manually" selected="True">manually</option>
222 <option value="bed_rgb">From the 9th field</option>
223 <option value="colormap">From the 5th field (score)</option>
224 </param>
225 <when value="manually">
226 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
227 </when>
228 <when value="bed_rgb" />
229 <when value="colormap">
230 <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">
231 <option value="RdYlBu">RdYlBu</option>
232 <option value="Accent">Accent</option>
233 <option value="Spectral">Spectral</option>
234 <option value="Set1">Set1</option>
235 <option value="Set2">Set2</option>
236 <option value="Set3">Set3</option>
237 <option value="Dark2">Dark2</option>
238 <option value="Reds">Reds</option>
239 <option value="Oranges">Oranges</option>
240 <option value="Greens">Greens</option>
241 <option value="Blues">Blues</option>
242 <option value="Greys">Greys</option>
243 <option value="Purples">Purples</option>
244 <option value="Paired">Paired</option>
245 <option value="Pastel1">Pastel1</option>
246 <option value="Pastel2">Pastel2</option>
247 <option value="spring">spring</option>
248 <option value="summer">summer</option>
249 <option value="autumn">autumn</option>
250 <option value="winter">winter</option>
251 <option value="hot">hot</option>
252 <option value="coolwarm">coolwarm</option>
253 <option value="cool">cool</option>
254 <option value="seismic">seismic</option>
255 <option value="terrain">terrain</option>
256 <option value="ocean">ocean</option>
257 <option value="rainbow">rainbow</option>
258 <option value="bone">bone</option>
259 <option value="flag">flag</option>
260 <option value="prism">prism</option>
261 <option value="cubehelix">cubehelix</option>
262 <option value="binary">binary</option>
263 <option value="pink">pink</option>
264 <option value="gray">gray</option>
265 <option value="copper">copper</option>
266 <option value="BrBG">BrBG</option>
267 <option value="BuGn">BuGn</option>
268 <option value="BuPu">BuPu</option>
269 <option value="GnBu">GnBu</option>
270 <option value="OrRd">OrRd</option>
271 <option value="PiYG">PiYG</option>
272 <option value="PRGn">PRGn</option>
273 <option value="PuOr">PuOr</option>
274 <option value="PuRd">PuRd</option>
275 <option value="PuBu">PuBu</option>
276 <option value="RdBu">RdBu</option>
277 <option value="RdGy">RdGy</option>
278 <option value="RdPu">RdPu</option>
279 <option value="YlGn">YlGn</option>
280 <option value="PuBuGn">PuBuGn</option>
281 <option value="RdYlGn">RdYlGn</option>
282 <option value="YlGnBu">YlGnBu</option>
283 <option value="YlOrBr">YlOrBr</option>
284 <option value="YlOrRd">YlOrRd</option>
285 <option value="gist_gray">gist_gray</option>
286 <option value="gist_stern">gist_stern</option>
287 <option value="gist_earth">gist_earth</option>
288 <option value="gist_yarg">gist_yarg</option>
289 <option value="gist_ncar">gist_ncar</option>
290 <option value="gist_rainbow">gist_rainbow</option>
291 <option value="gist_heat">gist_heat</option>
292 <option value="gnuplot">gnuplot</option>
293 <option value="gnuplot2">gnuplot2</option>
294 <option value="CMRmap">CMRmap</option>
295 <option value="bwr">bwr</option>
296 <option value="hsv">hsv</option>
297 <option value="brg">brg</option>
298 <option value="jet">jet</option>
299 <option value="afmhot">afmhot</option>
300 <option value="Accent_r">Accent reversed</option>
301 <option value="Spectral_r">Spectral reversed</option>
302 <option value="Set1_r">Set1 reversed</option>
303 <option value="Set2_r">Set2 reversed</option>
304 <option value="Set3_r">Set3 reversed</option>
305 <option value="Dark2_r">Dark2 reversed</option>
306 <option value="Reds_r">Reds reversed</option>
307 <option value="Oranges_r">Oranges reversed</option>
308 <option value="Greens_r">Greens reversed</option>
309 <option value="Blues_r">Blues reversed</option>
310 <option value="Greys_r">Greys reversed</option>
311 <option value="Purples_r">Purples reversed</option>
312 <option value="Paired_r">Paired reversed</option>
313 <option value="Pastel1_r">Pastel1 reversed</option>
314 <option value="Pastel2_r">Pastel2 reversed</option>
315 <option value="spring_r">spring reversed</option>
316 <option value="summer_r">summer reversed</option>
317 <option value="autumn_r">autumn reversed</option>
318 <option value="winter_r">winter reversed</option>
319 <option value="hot_r">hot reversed</option>
320 <option value="coolwarm_r">coolwarm reversed</option>
321 <option value="cool_r">cool reversed</option>
322 <option value="seismic_r">seismic reversed</option>
323 <option value="terrain_r">terrain reversed</option>
324 <option value="ocean_r">ocean reversed</option>
325 <option value="rainbow_r">rainbow reversed</option>
326 <option value="bone_r">bone reversed</option>
327 <option value="flag_r">flag reversed</option>
328 <option value="prism_r">prism reversed</option>
329 <option value="cubehelix_r">cubehelix reversed</option>
330 <option value="binary_r">binary reversed</option>
331 <option value="pink_r">pink reversed</option>
332 <option value="gray_r">gray reversed</option>
333 <option value="copper_r">copper reversed</option>
334 <option value="BrBG_r">BrBG reversed</option>
335 <option value="BuGn_r">BuGn reversed</option>
336 <option value="BuPu_r">BuPu reversed</option>
337 <option value="GnBu_r">GnBu reversed</option>
338 <option value="OrRd_r">OrRd reversed</option>
339 <option value="PiYG_r">PiYG reversed</option>
340 <option value="PRGn_r">PRGn reversed</option>
341 <option value="PuOr_r">PuOr reversed</option>
342 <option value="PuRd_r">PuRd reversed</option>
343 <option value="PuBu_r">PuBu reversed</option>
344 <option value="RdBu_r">RdBu reversed</option>
345 <option value="RdGy_r">RdGy reversed</option>
346 <option value="RdPu_r">RdPu reversed</option>
347 <option value="YlGn_r">YlGn reversed</option>
348 <option value="PuBuGn_r">PuBuGn reversed</option>
349 <option value="RdYlBu_r" selected="True">RdYlBu reversed</option>
350 <option value="RdYlGn_r">RdYlGn reversed</option>
351 <option value="YlGnBu_r">YlGnBu reversed</option>
352 <option value="YlOrBr_r">YlOrBr reversed</option>
353 <option value="YlOrRd_r">YlOrRd reversed</option>
354 <option value="gist_gray_r">gist_gray reversed</option>
355 <option value="gist_stern_r">gist_stern reversed</option>
356 <option value="gist_earth_r">gist_earth reversed</option>
357 <option value="gist_yarg_r">gist_yarg reversed</option>
358 <option value="gist_ncar_r">gist_ncar reversed</option>
359 <option value="gist_rainbow_r">gist_rainbow reversed</option>
360 <option value="gist_heat_r">gist_heat reversed</option>
361 <option value="gnuplot_r">gnuplot reversed</option>
362 <option value="gnuplot2_r">gnuplot2 reversed</option>
363 <option value="CMRmap_r">CMRmap reversed</option>
364 <option value="bwr_r">bwr reversed</option>
365 <option value="hsv_r">hsv reversed</option>
366 <option value="brg_r">brg reversed</option>
367 <option value="jet_r">jet reversed</option>
368 <option value="afmhot_r">afmhot reversed</option>
369 </param>
370 </when>
371 </conditional>
372 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
373 </xml>
374 <xml name="color_coverage_macro">
375 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
376 <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"/>
377 <conditional name="color_negative">
378 <param name="color_negative_select" type="select" label="Use a different color for negative values">
379 <option value="no" selected="True">No</option>
380 <option value="yes">Yes</option>
381 </param>
382 <when value="no" />
383 <when value="yes">
384 <param name="color" type="color" value="#000000" label="Color of negative values" optional="True" />
385 </when>
386 </conditional>
387 </xml>
388 <xml name="overlay_macro">
389 <param name="overlay_select" type="select" label="Overlay this track with the previous one:">
390 <option value="no" selected="True">No</option>
391 <option value="yes">Yes</option>
392 <option value="share-y">Yes and keep same y axis</option>
393 </param>
394 </xml>
395 <xml name="type_coverage_macro">
396 <conditional name="type_conditional">
397 <param name="type_selector" type="select" label="Choose style of the plot.">
398 <option value="fill_option">fill</option>
399 <option value="line_option">line</option>
400 <option value="point_option">point</option>
401 </param>
402 <when value="line_option">
403 <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
404 </when>
405 <when value="point_option">
406 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
407 </when>
408 <when value="fill_option" />
409 </conditional>
410 </xml>
411 <xml name="minmax_macro">
412 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
413 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
414 </xml>
415 <xml name="reading_bw_macro">
416 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
417 <param name="summary" type="select" label="Summary method">
418 <option value="mean" selected="True">mean=mean value</option>
419 <option value="min">min=minimum value</option>
420 <option value="max">max=maximum value</option>
421 <option value="coverage">coverage=number of covered bases</option>
422 <option value="std">std=standard deviation</option>
423 </param>
424 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
425 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
426 label="NAN's to zeros" />
427 </section>
428 </xml>
210 </macros> 429 </macros>