Mercurial > repos > iuc > pygenometracks

comparison pyGenomeTracks.xml @ 6:5cec5fb749f0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d5b42c5571c64be9fcfe515e79210cbf4c75beaf"
author iuc
date Tue, 11 Feb 2020 10:20:24 -0500
parents eca03db4f612
children 326a3db8d9d1
comparison
equal deleted inserted replaced
5:eca03db4f612 6:5cec5fb749f0
65 depth = $track.track_file_style_conditional.depth 65 depth = $track.track_file_style_conditional.depth
66 #end if 66 #end if
67 #if $track.track_file_style_conditional.colormap: 67 #if $track.track_file_style_conditional.colormap:
68 colormap = $track.track_file_style_conditional.colormap 68 colormap = $track.track_file_style_conditional.colormap
69 #end if 69 #end if
70 #if $track.track_file_style_conditional.min_value: 70 #if $track.track_file_style_conditional.min_value != "":
71 min_value = $track.track_file_style_conditional.min_value 71 min_value = $track.track_file_style_conditional.min_value
72 #end if 72 #end if
73 #if $track.track_file_style_conditional.max_value: 73 #if $track.track_file_style_conditional.max_value != "":
74 max_value = $track.track_file_style_conditional.max_value 74 max_value = $track.track_file_style_conditional.max_value
75 #end if 75 #end if
76 transform = $track.track_file_style_conditional.transform 76 transform = $track.track_file_style_conditional.transform
77 #if $track.track_file_style_conditional.height_matrix != "": 77 #if $track.track_file_style_conditional.height_matrix != "":
78 height = $track.track_file_style_conditional.height_matrix 78 height = $track.track_file_style_conditional.height_matrix
210 title = $track.track_file_style_conditional.track_input_link.name 210 title = $track.track_file_style_conditional.track_input_link.name
211 #end if 211 #end if
212 #if $track.track_file_style_conditional.height: 212 #if $track.track_file_style_conditional.height:
213 height = $track.track_file_style_conditional.height 213 height = $track.track_file_style_conditional.height
214 #end if 214 #end if
215 #if $track.track_file_style_conditional.min_value: 215 #if $track.track_file_style_conditional.min_value != "":
216 min_value = $track.track_file_style_conditional.min_value 216 min_value = $track.track_file_style_conditional.min_value
217 #end if 217 #end if
218 #if $track.track_file_style_conditional.max_value: 218 #if $track.track_file_style_conditional.max_value != "":
219 max_value = $track.track_file_style_conditional.max_value 219 max_value = $track.track_file_style_conditional.max_value
220 #end if 220 #end if
221 color = $track.track_file_style_conditional.color_link.color 221 color = $track.track_file_style_conditional.color_link.color
222 alpha = $track.track_file_style_conditional.alpha 222 alpha = $track.track_file_style_conditional.alpha
223 line_width = $track.track_file_style_conditional.line_width 223 line_width = $track.track_file_style_conditional.line_width
251 #if $track.track_file_style_conditional.display.display_selector == "peak": 251 #if $track.track_file_style_conditional.display.display_selector == "peak":
252 show_data_range = $track.track_file_style_conditional.display.show_data 252 show_data_range = $track.track_file_style_conditional.display.show_data
253 #if $track.track_file_style_conditional.display.width_adjust: 253 #if $track.track_file_style_conditional.display.width_adjust:
254 width_adjust = $track.track_file_style_conditional.display.width_adjust 254 width_adjust = $track.track_file_style_conditional.display.width_adjust
255 #end if 255 #end if
256 #if $track.track_file_style_conditional.display.min_value: 256 #if $track.track_file_style_conditional.display.min_value != "":
257 min_value = $track.track_file_style_conditional.display.min_value 257 min_value = $track.track_file_style_conditional.display.min_value
258 #end if 258 #end if
259 #if $track.track_file_style_conditional.display.max_value: 259 #if $track.track_file_style_conditional.display.max_value != "":
260 max_value = $track.track_file_style_conditional.display.max_value 260 max_value = $track.track_file_style_conditional.display.max_value
261 #end if 261 #end if
262 #end if 262 #end if
263 #if $track.track_file_style_conditional.height_narrow_peak: 263 #if $track.track_file_style_conditional.height_narrow_peak:
264 height = $track.track_file_style_conditional.height_narrow_peak 264 height = $track.track_file_style_conditional.height_narrow_peak
298 negative_color = $track.track_file_style_conditional.color_negative.color 298 negative_color = $track.track_file_style_conditional.color_negative.color
299 #end if 299 #end if
300 #if $track.track_file_style_conditional.height_bedgraph: 300 #if $track.track_file_style_conditional.height_bedgraph:
301 height = $track.track_file_style_conditional.height_bedgraph 301 height = $track.track_file_style_conditional.height_bedgraph
302 #end if 302 #end if
303 #if $track.track_file_style_conditional.min_value: 303 #if $track.track_file_style_conditional.min_value != "":
304 min_value = $track.track_file_style_conditional.min_value 304 min_value = $track.track_file_style_conditional.min_value
305 #end if 305 #end if
306 #if $track.track_file_style_conditional.max_value: 306 #if $track.track_file_style_conditional.max_value != "":
307 max_value = $track.track_file_style_conditional.max_value 307 max_value = $track.track_file_style_conditional.max_value
308 #end if 308 #end if
309 show_data_range = $track.track_file_style_conditional.show_data 309 show_data_range = $track.track_file_style_conditional.show_data
310 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros 310 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros
311 use_middle = $track.track_file_style_conditional.use_middle 311 use_middle = $track.track_file_style_conditional.use_middle
350 #end if 350 #end if
351 alpha = $track.track_file_style_conditional.alpha 351 alpha = $track.track_file_style_conditional.alpha
352 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true": 352 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
353 negative_color = $track.track_file_style_conditional.color_negative.color 353 negative_color = $track.track_file_style_conditional.color_negative.color
354 #end if 354 #end if
355 #if $track.track_file_style_conditional.min_value: 355 #if $track.track_file_style_conditional.min_value != "":
356 min_value = $track.track_file_style_conditional.min_value 356 min_value = $track.track_file_style_conditional.min_value
357 #end if 357 #end if
358 #if $track.track_file_style_conditional.max_value: 358 #if $track.track_file_style_conditional.max_value != "":
359 max_value = $track.track_file_style_conditional.max_value 359 max_value = $track.track_file_style_conditional.max_value
360 #end if 360 #end if
361 height = $track.track_file_style_conditional.height_bigwig 361 height = $track.track_file_style_conditional.height_bigwig
362 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary 362 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary
363 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros 363 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
396 title = $data_bedgraph_matrix.name 396 title = $data_bedgraph_matrix.name
397 #end if 397 #end if
398 #if $track.track_file_style_conditional.height_bedgraph: 398 #if $track.track_file_style_conditional.height_bedgraph:
399 height = $track.track_file_style_conditional.height_bedgraph 399 height = $track.track_file_style_conditional.height_bedgraph
400 #end if 400 #end if
401 #if $track.track_file_style_conditional.min_value: 401 #if $track.track_file_style_conditional.min_value != "":
402 min_value = $track.track_file_style_conditional.min_value 402 min_value = $track.track_file_style_conditional.min_value
403 #end if 403 #end if
404 #if $track.track_file_style_conditional.max_value: 404 #if $track.track_file_style_conditional.max_value != "":
405 max_value = $track.track_file_style_conditional.max_value 405 max_value = $track.track_file_style_conditional.max_value
406 #end if 406 #end if
407 #if $track.track_file_style_conditional.type_lines: 407 #if $track.track_file_style_conditional.type_lines:
408 type = $track.track_file_style_conditional.type_lines 408 type = $track.track_file_style_conditional.type_lines
409 #end if 409 #end if
436 title = $track.track_file_style_conditional.title 436 title = $track.track_file_style_conditional.title
437 #end if 437 #end if
438 #if $track.track_file_style_conditional.height: 438 #if $track.track_file_style_conditional.height:
439 height = $track.track_file_style_conditional.height 439 height = $track.track_file_style_conditional.height
440 #end if 440 #end if
441 #if $track.track_file_style_conditional.min_value: 441 #if $track.track_file_style_conditional.min_value != "":
442 min_value = $track.track_file_style_conditional.min_value 442 min_value = $track.track_file_style_conditional.min_value
443 #end if 443 #end if
444 #if $track.track_file_style_conditional.max_value: 444 #if $track.track_file_style_conditional.max_value != "":
445 max_value = $track.track_file_style_conditional.max_value 445 max_value = $track.track_file_style_conditional.max_value
446 #end if 446 #end if
447 y_values = $track.track_file_style_conditional.y_values 447 y_values = $track.track_file_style_conditional.y_values
448 show_data_range = $track.track_file_style_conditional.show_data 448 show_data_range = $track.track_file_style_conditional.show_data
449 color = $track.track_file_style_conditional.color 449 color = $track.track_file_style_conditional.color
517 517
518 </param> 518 </param>
519 <param name="height_matrix" type="float" value="" optional="True" label="height"/> 519 <param name="height_matrix" type="float" value="" optional="True" label="height"/>
520 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false" 520 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false"
521 label="Show masked bins" /> 521 label="Show masked bins" />
522 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/> 522 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/>
523 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> 523 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
524 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true" 524 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true"
525 label="Rasterize the heatmap" /> 525 label="Rasterize the heatmap" />
526 <expand macro="inverted_macro" /> 526 <expand macro="inverted_macro" />
527 <expand macro="spacer_macro" /> 527 <expand macro="spacer_macro" />
552 <option value="interleaved">interleaved (everything on 2 lines)</option> 552 <option value="interleaved">interleaved (everything on 2 lines)</option>
553 <option value="collapsed">collapsed (everything on 1 line)</option> 553 <option value="collapsed">collapsed (everything on 1 line)</option>
554 <option value="triangles">triangles (plot triangles between start and end)</option> 554 <option value="triangles">triangles (plot triangles between start and end)</option>
555 </param> 555 </param>
556 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false" 556 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
557 label="Include the arrowhead in the bed interval:" 557 label="Include the arrowhead in the bed interval:"
558 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/> 558 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
559 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 559 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
560 <expand macro="bed_advanced_macro" /> 560 <expand macro="bed_advanced_macro" />
561 <expand macro="overlay_macro" /> 561 <expand macro="overlay_macro" />
562 <expand macro="inverted_macro" /> 562 <expand macro="inverted_macro" />
570 <expand macro="lines_macro" /> 570 <expand macro="lines_macro" />
571 <param name="links_type" type="select" label="Representation of the link:"> 571 <param name="links_type" type="select" label="Representation of the link:">
572 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option> 572 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
573 <option value="triangles">triangles</option> 573 <option value="triangles">triangles</option>
574 <option value="loops">loops (a rectangle highlighting the intersection)</option> 574 <option value="loops">loops (a rectangle highlighting the intersection)</option>
575 </param> 575 </param>
576 <param name="height" type="float" value="1.5" optional="True" label="height"/> 576 <param name="height" type="float" value="1.5" optional="True" label="height"/>
577 <expand macro="minmax_macro" /> 577 <expand macro="minmax_macro" />
578 <expand macro="overlay_macro" /> 578 <expand macro="overlay_macro" />
579 <expand macro="inverted_macro" /> 579 <expand macro="inverted_macro" />
580 <expand macro="spacer_macro" /> 580 <expand macro="spacer_macro" />
581 </when> 581 </when>
582 <when value="narrow_peak_track_option"> 582 <when value="narrow_peak_track_option">
583 <expand macro="plot_title" /> 583 <expand macro="plot_title" />
584 <expand macro="track_input_narrow_peak_macro" /> 584 <expand macro="track_input_narrow_peak_macro" />
585 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 585 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
586 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/> 586 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/>
592 <when value="peak"> 592 <when value="peak">
593 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" 593 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
594 optional="True" label="Use summit information to make the curve." /> 594 optional="True" label="Use summit information to make the curve." />
595 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" 595 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
596 label="Show visualization of data range" /> 596 label="Show visualization of data range" />
597 <param name="width_adjust" type="float" value="1.5" optional="True" 597 <param name="width_adjust" type="float" value="1.5" optional="True"
598 label="Factor to change the width of the curve."/> 598 label="Factor to change the width of the curve."/>
599 <expand macro="minmax_macro" /> 599 <expand macro="minmax_macro" />
600 </when> 600 </when>
601 <when value="box"> 601 <when value="box">
602 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true" 602 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
678 <param name="height" type="float" value="1.5" optional="True" label="height"/> 678 <param name="height" type="float" value="1.5" optional="True" label="height"/>
679 <expand macro="minmax_macro" /> 679 <expand macro="minmax_macro" />
680 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> 680 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
681 <expand macro="inverted_macro" /> 681 <expand macro="inverted_macro" />
682 <expand macro="overlay_macro" /> 682 <expand macro="overlay_macro" />
683 <expand macro="spacer_macro" /> 683 <expand macro="spacer_macro" />
684 </when> 684 </when>
685 <when value="spacer_option"> 685 <when value="spacer_option">
686 <param name="spacer_height" type="float" value="" optional="True" 686 <param name="spacer_height" type="float" value="" optional="True"
687 label="Height of the spacer."/> 687 label="Height of the spacer."/>
688 </when> 688 </when>