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comparison pyGenomeTracks.xml @ 8:4ac4e7083b7e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
author iuc
date Tue, 21 Jul 2020 03:32:48 -0400
parents 326a3db8d9d1
children 2824d77cd8f8
comparison
equal deleted inserted replaced
7:326a3db8d9d1 8:4ac4e7083b7e
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 ## First symlink data of hic or bed/gtf to have the good extension 10 ## First symlink data of hic to have the good extension
11 #for $counter, $track in enumerate($tracks): 11 #for $counter, $track in enumerate($tracks):
12 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": 12 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
13 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): 13 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
14 #set ext = $data_matrix.extension 14 #set ext = $data_matrix.extension
15 ln -s $data_matrix ${counter}_${counter_matrix}.$ext && 15 ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&
16 #end for
17 #end if
18 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
19 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
20 #set ext = $data_bed.extension
21 ln -s $data_bed ${counter}_${counter_bed}.$ext &&
22 #end for 16 #end for
23 #end if 17 #end if
24 #end for 18 #end for
25 19
26 20
36 --fontSize $global_args.fontsize 30 --fontSize $global_args.fontsize
37 --dpi $global_args.dpi 31 --dpi $global_args.dpi
38 --trackLabelFraction $global_args.trackLabelFraction 32 --trackLabelFraction $global_args.trackLabelFraction
39 --trackLabelHAlign $global_args.trackLabelHAlign 33 --trackLabelHAlign $global_args.trackLabelHAlign
40 --outFileName plot.$image_file_format 34 --outFileName plot.$image_file_format
35 $global_args.decreasingXAxis
41 && mv plot.$image_file_format plot 36 && mv plot.$image_file_format plot
42 ]]> 37 ]]>
43 </command> 38 </command>
44 <configfiles> 39 <configfiles>
45 <configfile name="tracks_config"> 40 <configfile name="tracks_config">
142 ## Gene/gtf track 137 ## Gene/gtf track
143 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": 138 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
144 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed): 139 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
145 [genes_${counter}_${counter_bed}] 140 [genes_${counter}_${counter_bed}]
146 #set ext = $data_bed.extension 141 #set ext = $data_bed.extension
147 file = ${counter}_${counter_bed}.$ext 142 file = $data_bed
148 #if $ext == 'gtf': 143 #if $ext == 'gtf':
149 prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name 144 prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name
150 merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts 145 merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts
151 #end if 146 #end if
152 #if $track.track_file_style_conditional.title: 147 #if $track.track_file_style_conditional.title:
194 labels = $track.track_file_style_conditional.labels.plot_labels 189 labels = $track.track_file_style_conditional.labels.plot_labels
195 #if $track.track_file_style_conditional.labels.plot_labels == 'true': 190 #if $track.track_file_style_conditional.labels.plot_labels == 'true':
196 all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside 191 all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside
197 labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin 192 labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin
198 #end if 193 #end if
199 file_type = bed 194 file_type = $ext
200 #if $track.track_file_style_conditional.fontsize: 195 #if $track.track_file_style_conditional.fontsize:
201 fontsize = $track.track_file_style_conditional.fontsize 196 fontsize = $track.track_file_style_conditional.fontsize
202 #end if 197 #end if
203 #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows: 198 #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows:
204 gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows 199 gene_rows = $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows
243 links_type = $track.track_file_style_conditional.links_type 238 links_type = $track.track_file_style_conditional.links_type
244 compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level 239 compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level
245 #if $track.track_file_style_conditional.ylim != "": 240 #if $track.track_file_style_conditional.ylim != "":
246 ylim = $track.track_file_style_conditional.ylim 241 ylim = $track.track_file_style_conditional.ylim
247 #end if 242 #end if
243 use_middle = $track.track_file_style_conditional.use_middle
248 #if $track.track_file_style_conditional.invert_orientation: 244 #if $track.track_file_style_conditional.invert_orientation:
249 orientation = inverted 245 orientation = inverted
250 #end if 246 #end if
251 overlay_previous = $track.track_file_style_conditional.overlay_select 247 overlay_previous = $track.track_file_style_conditional.overlay_select
252 file_type = links 248 file_type = links
328 #end if 324 #end if
329 #if $track.track_file_style_conditional.max_value != "": 325 #if $track.track_file_style_conditional.max_value != "":
330 max_value = $track.track_file_style_conditional.max_value 326 max_value = $track.track_file_style_conditional.max_value
331 #end if 327 #end if
332 show_data_range = $track.track_file_style_conditional.show_data 328 show_data_range = $track.track_file_style_conditional.show_data
329 grid = $track.track_file_style_conditional.grid
333 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros 330 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros
334 use_middle = $track.track_file_style_conditional.use_middle 331 use_middle = $track.track_file_style_conditional.use_middle
335 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) 332 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
336 #if $columns > 4: 333 #if $columns > 4:
337 file_type = bedgraph_matrix 334 file_type = bedgraph_matrix
343 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': 340 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
344 type = line:$track.track_file_style_conditional.type_conditional.width_line 341 type = line:$track.track_file_style_conditional.type_conditional.width_line
345 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': 342 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
346 type = points:$track.track_file_style_conditional.type_conditional.width_point 343 type = points:$track.track_file_style_conditional.type_conditional.width_point
347 #end if 344 #end if
345 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
346 transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
347 y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
348 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
349 log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
350 #end if
351 #end if
352 #end if
353 #if $track.track_file_style_conditional.reading_bdg_as_bw.summary_method != 'no':
354 summary_method = $track.track_file_style_conditional.reading_bdg_as_bw.summary_method
355 #if $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins:
356 number_of_bins = $track.track_file_style_conditional.reading_bdg_as_bw.number_of_bins
357 #end if
358 #end if
359 #if $track.track_file_style_conditional.op.operation != 'file':
360 operation = $track.track_file_style_conditional.op.operation
361 #if 'second_file' in str($track.track_file_style_conditional.op.operation):
362 second_file = $track.track_file_style_conditional.op.second_file
363 #end if
348 #end if 364 #end if
349 #if $track.track_file_style_conditional.invert_orientation: 365 #if $track.track_file_style_conditional.invert_orientation:
350 orientation = inverted 366 orientation = inverted
351 #end if 367 #end if
352 overlay_previous = $track.track_file_style_conditional.overlay_select 368 overlay_previous = $track.track_file_style_conditional.overlay_select
380 #end if 396 #end if
381 #if $track.track_file_style_conditional.max_value != "": 397 #if $track.track_file_style_conditional.max_value != "":
382 max_value = $track.track_file_style_conditional.max_value 398 max_value = $track.track_file_style_conditional.max_value
383 #end if 399 #end if
384 height = $track.track_file_style_conditional.height_bigwig 400 height = $track.track_file_style_conditional.height_bigwig
385 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary 401 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary_method
386 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros 402 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
387 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: 403 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
388 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins 404 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
389 #end if 405 #end if
390 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': 406 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
392 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': 408 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
393 type = line:$track.track_file_style_conditional.type_conditional.width_line 409 type = line:$track.track_file_style_conditional.type_conditional.width_line
394 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': 410 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
395 type = points:$track.track_file_style_conditional.type_conditional.width_point 411 type = points:$track.track_file_style_conditional.type_conditional.width_point
396 #end if 412 #end if
413 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'no':
414 transform = $track.track_file_style_conditional.logScale_conditional.transform_selector
415 y_axis_values = $track.track_file_style_conditional.logScale_conditional.y_axis_values
416 #if $track.track_file_style_conditional.logScale_conditional.transform_selector != 'log1p':
417 log_pseudocount = $track.track_file_style_conditional.logScale_conditional.log_pseudocount
418 #end if
419 #end if
420 #if $track.track_file_style_conditional.op.operation != 'file':
421 operation = $track.track_file_style_conditional.op.operation
422 #if 'second_file' in $track.track_file_style_conditional.op.operation:
423 second_file = $track.track_file_style_conditional.op.second_file
424 #end if
425 #end if
397 show_data_range = $track.track_file_style_conditional.show_data 426 show_data_range = $track.track_file_style_conditional.show_data
427 grid = $track.track_file_style_conditional.grid
398 file_type = bigwig 428 file_type = bigwig
399 #if $track.track_file_style_conditional.invert_orientation: 429 #if $track.track_file_style_conditional.invert_orientation:
400 orientation = inverted 430 orientation = inverted
401 #end if 431 #end if
402 overlay_previous = $track.track_file_style_conditional.overlay_select 432 overlay_previous = $track.track_file_style_conditional.overlay_select
449 479
450 ## Vlines: 480 ## Vlines:
451 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": 481 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
452 [vlines_$counter] 482 [vlines_$counter]
453 file = $track.track_file_style_conditional.track_input_bed_single 483 file = $track.track_file_style_conditional.track_input_bed_single
484 line_width = $track.track_file_style_conditional.line_width
454 type = vlines 485 type = vlines
455 #end if 486 #end if
456 487
457 ## Hlines: 488 ## Hlines:
458 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option": 489 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option":
560 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels"> 591 <param argument="--trackLabelHAlign" type="select" label="Horizontal alignment of track labels">
561 <option value="left" selected="True">left</option> 592 <option value="left" selected="True">left</option>
562 <option value="right">right</option> 593 <option value="right">right</option>
563 <option value="center">center</option> 594 <option value="center">center</option>
564 </param> 595 </param>
596 <param argument="--decreasingXAxis" type="boolean" truevalue="--decreasingXAxis" falsevalue="" checked="false"
597 label="Use a decreasing x axis" help="By default, the x-axis is increasing. Use this option if you want to see all tracks with a decreasing x-axis."/>
565 </section> 598 </section>
566 <!--Info to build the config file--> 599 <!--Info to build the config file-->
567 <repeat name="tracks" min="1" title="Include tracks in your plot" 600 <repeat name="tracks" min="1" title="Include tracks in your plot"
568 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph. 601 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph.
569 The order you add them represent the order they will be plotted from top to bottom."> 602 The order you add them represent the order they will be plotted from top to bottom.">
744 <option value="0" selected="True">default (proportional to distance)</option> 777 <option value="0" selected="True">default (proportional to distance)</option>
745 <option value="1">compacted (the height is proportional to the square root of the distance)</option> 778 <option value="1">compacted (the height is proportional to the square root of the distance)</option>
746 <option value="2">highly compacted (the height is the same for all distances)</option> 779 <option value="2">highly compacted (the height is the same for all distances)</option>
747 </param> 780 </param>
748 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/> 781 <param name="ylim" type="float" optional="True" label="ylim" help="To be able to see small arcs when big arcs exists, you can set the upper y limit. The unit is bp. This corresponds to the longest arc you will see not truncated."/>
782 <param name="use_middle" type="select" label="Coordinates to use" help="Not useful with loops">
783 <option value="false" selected="True">Extremities (start of first and end of second)</option>
784 <option value="true">Center (mean of start and end for each)</option>
785 </param>
749 <param name="height" type="float" value="1.5" optional="True" label="height"/> 786 <param name="height" type="float" value="1.5" optional="True" label="height"/>
750 <expand macro="minmax_macro" /> 787 <expand macro="minmax_macro" />
751 <expand macro="overlay_macro" /> 788 <expand macro="overlay_macro" />
752 <expand macro="inverted_macro" /> 789 <expand macro="inverted_macro" />
753 <expand macro="spacer_macro" /> 790 <expand macro="spacer_macro" />
790 <expand macro="track_input_bedgraph_macro" /> 827 <expand macro="track_input_bedgraph_macro" />
791 <expand macro="color_coverage_macro" /> 828 <expand macro="color_coverage_macro" />
792 <expand macro="minmax_macro" /> 829 <expand macro="minmax_macro" />
793 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> 830 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
794 <expand macro="type_coverage_macro" /> 831 <expand macro="type_coverage_macro" />
832 <section name="reading_bdg_as_bw" title="Configure bigwig parameters" expanded="False">
833 <param name="summary_method" type="select" label="Summary method">
834 <option value="no" selected="True">no=no summary method (keep all values)</option>
835 <option value="mean">mean=mean value</option>
836 <option value="min">min=minimum value</option>
837 <option value="max">max=maximum value</option>
838 <option value="coverage">coverage=number of covered bases</option>
839 <option value="std">std=standard deviation</option>
840 </param>
841 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
842 </section>
843 <expand macro="logScale_coverage_macro" />
844 <section name ="op" title="Compute an operation on the file" expanded="False">
845 <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
846 help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
847 <param name="second_file" type="data" format="bedgraph" label="second_file (bedgraph format)" multiple="False" optional="True"/>
848 </section>
795 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" 849 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
796 label="NAN's to zeros" /> 850 label="NAN's to zeros" />
797 <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false" 851 <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false"
798 label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." /> 852 label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." />
799 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" /> 853 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" />
854 <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
800 <expand macro="inverted_macro" /> 855 <expand macro="inverted_macro" />
801 <expand macro="overlay_macro" /> 856 <expand macro="overlay_macro" />
802 <expand macro="spacer_macro" /> 857 <expand macro="spacer_macro" />
803 </when> 858 </when>
804 <when value="bigwig_track_option"> 859 <when value="bigwig_track_option">
809 864
810 <expand macro="minmax_macro" /> 865 <expand macro="minmax_macro" />
811 866
812 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> 867 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
813 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False"> 868 <section name="reading_bw_conditional" title="Configure bigwig parameters" expanded="False">
814 <param name="summary" type="select" label="Summary method"> 869 <param name="summary_method" type="select" label="Summary method">
815 <option value="mean" selected="True">mean=mean value</option> 870 <option value="mean" selected="True">mean=mean value</option>
816 <option value="min">min=minimum value</option> 871 <option value="min">min=minimum value</option>
817 <option value="max">max=maximum value</option> 872 <option value="max">max=maximum value</option>
818 <option value="coverage">coverage=number of covered bases</option> 873 <option value="coverage">coverage=number of covered bases</option>
819 <option value="std">std=standard deviation</option> 874 <option value="std">std=standard deviation</option>
821 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> 876 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
822 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false" 877 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
823 label="NAN's to zeros" /> 878 label="NAN's to zeros" />
824 </section> 879 </section>
825 <expand macro="type_coverage_macro" /> 880 <expand macro="type_coverage_macro" />
881 <expand macro="logScale_coverage_macro" />
882 <section name ="op" title="Compute an operation on the file" expanded="False">
883 <param name="operation" type="text" label="operation to compute on the file(s)" value="file"
884 help="operation will be evaluated, it should contains file or file and second_file, for example `0.89 * file` `- file` `file - second_file` `log2((1 + file) / (1 + second_file))` or `max(file, second_file)`"/>
885 <param name="second_file" type="data" format="bigwig" label="second_file (bedgraph format)" multiple="False" optional="True"/>
886 </section>
826 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/> 887 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
888 <param name="grid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Display a grid on the y-axis" />
827 <expand macro="inverted_macro" /> 889 <expand macro="inverted_macro" />
828 <expand macro="overlay_macro" /> 890 <expand macro="overlay_macro" />
829 <expand macro="spacer_macro" /> 891 <expand macro="spacer_macro" />
830 892
831 </when> 893 </when>
866 <expand macro="spacer_macro" /> 928 <expand macro="spacer_macro" />
867 929
868 </when> 930 </when>
869 <when value="vlines_track_option"> 931 <when value="vlines_track_option">
870 <expand macro="track_input_bed_single_macro" /> 932 <expand macro="track_input_bed_single_macro" />
933 <param name="line_width" type="float" value="0.5" label="width of lines"/>
871 </when> 934 </when>
872 <when value="hlines_track_option"> 935 <when value="hlines_track_option">
873 <expand macro="plot_title" /> 936 <expand macro="plot_title" />
874 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/> 937 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/>
875 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" /> 938 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" />
1278 <conditional name="type_conditional"> 1341 <conditional name="type_conditional">
1279 <param name="type_selector" value="point_option" /> 1342 <param name="type_selector" value="point_option" />
1280 <param name="width_point" value="5" /> 1343 <param name="width_point" value="5" />
1281 </conditional> 1344 </conditional>
1282 <section name="reading_bw_conditional"> 1345 <section name="reading_bw_conditional">
1283 <param name="summary" value="max"/> 1346 <param name="summary_method" value="max"/>
1284 <param name="number_of_bins" value="100"/> 1347 <param name="number_of_bins" value="100"/>
1285 </section> 1348 </section>
1286 </conditional> 1349 </conditional>
1287 </repeat> 1350 </repeat>
1288 <repeat name="tracks"> 1351 <repeat name="tracks">
1293 <param name="color" value="#c00000" /> 1356 <param name="color" value="#c00000" />
1294 <conditional name="type_conditional"> 1357 <conditional name="type_conditional">
1295 <param name="type_selector" value="line_option" /> 1358 <param name="type_selector" value="line_option" />
1296 </conditional> 1359 </conditional>
1297 <section name="reading_bw_conditional"> 1360 <section name="reading_bw_conditional">
1298 <param name="summary" value="min"/> 1361 <param name="summary_method" value="min"/>
1299 </section> 1362 </section>
1300 <param name="overlay_select" value="share-y" /> 1363 <param name="overlay_select" value="share-y" />
1301 </conditional> 1364 </conditional>
1302 </repeat> 1365 </repeat>
1303 <repeat name="tracks"> 1366 <repeat name="tracks">
1308 <param name="color" value="black" /> 1371 <param name="color" value="black" />
1309 <conditional name="type_conditional"> 1372 <conditional name="type_conditional">
1310 <param name="type_selector" value="line_option" /> 1373 <param name="type_selector" value="line_option" />
1311 </conditional> 1374 </conditional>
1312 <section name="reading_bw_conditional"> 1375 <section name="reading_bw_conditional">
1313 <param name="summary" value="min"/> 1376 <param name="summary_method" value="min"/>
1314 <param name="number_of_bins" value="30000"/> 1377 <param name="number_of_bins" value="30000"/>
1315 </section> 1378 </section>
1316 <param name="overlay_select" value="share-y" /> 1379 <param name="overlay_select" value="share-y" />
1317 <param name="spacer_height" value="1" /> 1380 <param name="spacer_height" value="1" />
1318 </conditional> 1381 </conditional>
1428 <param name="track_file_style_selector" value="bigwig_track_option" /> 1491 <param name="track_file_style_selector" value="bigwig_track_option" />
1429 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 1492 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
1430 <param name="title" value="" /> 1493 <param name="title" value="" />
1431 <param name="color" value="#ff0000" /> 1494 <param name="color" value="#ff0000" />
1432 <param name="alpha" value="0.5" /> 1495 <param name="alpha" value="0.5" />
1433 <param name="summary" value="max" /> 1496 <param name="summary_method" value="max" />
1434 <section name="reading_bw_conditional"> 1497 <section name="reading_bw_conditional">
1435 <param name="number_of_bins" value="300"/> 1498 <param name="number_of_bins" value="300"/>
1436 </section> 1499 </section>
1437 <param name="overlay_select" value="share-y"/> 1500 <param name="overlay_select" value="share-y"/>
1438 </conditional> 1501 </conditional>
2069 </conditional> 2132 </conditional>
2070 </repeat> 2133 </repeat>
2071 <param name="image_file_format" value="png" /> 2134 <param name="image_file_format" value="png" />
2072 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" /> 2135 <output name="outFileName" file="test_tssarrow.png" ftype="png" compare="sim_size" delta="35000" />
2073 </test> 2136 </test>
2137 <!--test 16-->
2138 <test>
2139 <param name="region" value="X:2700000-3100000"/>
2140 <section name="global_args">
2141 <param name="decreasingXAxis" value="true"/>
2142 </section>
2143 <repeat name="tracks">
2144 <conditional name="track_file_style_conditional">
2145 <param name="track_file_style_selector" value="bigwig_track_option" />
2146 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2147 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
2148 <param name="height_bigwig" value="7" />
2149 <param name="color" value="#00b0f0" />
2150 <section name="reading_bw_conditional">
2151 <param name="number_of_bins" value="2000"/>
2152 </section>
2153 </conditional>
2154 </repeat>
2155 <repeat name="tracks">
2156 <conditional name="track_file_style_conditional">
2157 <param name="track_file_style_selector" value="bigwig_track_option" />
2158 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
2159 <param name="title" value="" />
2160 <param name="color" value="#ff0000" />
2161 <param name="alpha" value="0.5" />
2162 <param name="summary_method" value="max" />
2163 <section name="reading_bw_conditional">
2164 <param name="number_of_bins" value="300"/>
2165 </section>
2166 <param name="overlay_select" value="share-y"/>
2167 </conditional>
2168 </repeat>
2169 <repeat name="tracks">
2170 <conditional name="track_file_style_conditional">
2171 <param name="track_file_style_selector" value="xaxis_option" />
2172 <param name="xaxis_where" value="bottom" />
2173 </conditional>
2174 </repeat>
2175 <param name="image_file_format" value="png" />
2176 <output name="outFileName" file="test_alpha_dec.png" ftype="png" compare="sim_size" delta="35000" />
2177 </test>
2178 <!--test 17-->
2179 <test>
2180 <param name="region" value="chr2:73,800,000-75,744,000"/>
2181 <repeat name="tracks">
2182 <conditional name="track_file_style_conditional">
2183 <param name="track_file_style_selector" value="bedgraph_track_option" />
2184 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2185 <param name="title" value="bedgraph color = blue transform = no" />
2186 <param name="height_bedgraph" value="5" />
2187 <param name="color" value="blue" />
2188 <param name="show_data" value="true" />
2189 </conditional>
2190 </repeat>
2191 <repeat name="tracks">
2192 <conditional name="track_file_style_conditional">
2193 <param name="track_file_style_selector" value="bedgraph_track_option" />
2194 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2195 <param name="title" value="bedgraph color = blue transform = log" />
2196 <param name="height_bedgraph" value="5" />
2197 <param name="color" value="blue" />
2198 <conditional name="logScale_conditional">
2199 <param name="transform_selector" value="log"/>
2200 </conditional>
2201 <param name="show_data" value="true" />
2202 </conditional>
2203 </repeat>
2204 <repeat name="tracks">
2205 <conditional name="track_file_style_conditional">
2206 <param name="track_file_style_selector" value="bedgraph_track_option" />
2207 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2208 <param name="title" value="bedgraph color = red transform = log min_value = 1" />
2209 <param name="height_bedgraph" value="5" />
2210 <param name="color" value="red" />
2211 <conditional name="logScale_conditional">
2212 <param name="transform_selector" value="log"/>
2213 </conditional>
2214 <param name="min_value" value="1" />
2215 <param name="show_data" value="true" />
2216 </conditional>
2217 </repeat>
2218 <repeat name="tracks">
2219 <conditional name="track_file_style_conditional">
2220 <param name="track_file_style_selector" value="bedgraph_track_option" />
2221 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2222 <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
2223 <param name="height_bedgraph" value="5" />
2224 <param name="color" value="green" />
2225 <conditional name="logScale_conditional">
2226 <param name="transform_selector" value="log"/>
2227 <param name="log_pseudocount" value="2"/>
2228 </conditional>
2229 <param name="min_value" value="0" />
2230 <param name="show_data" value="true" />
2231 </conditional>
2232 </repeat>
2233 <repeat name="tracks">
2234 <conditional name="track_file_style_conditional">
2235 <param name="track_file_style_selector" value="bedgraph_track_option" />
2236 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2237 <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
2238 <param name="height_bedgraph" value="5" />
2239 <param name="color" value="green" />
2240 <section name="op">
2241 <param name="operation" value="log(2+file)" />
2242 </section>
2243 <param name="min_value" value="0.7" />
2244 <param name="show_data" value="true" />
2245 </conditional>
2246 </repeat>
2247 <repeat name="tracks">
2248 <conditional name="track_file_style_conditional">
2249 <param name="track_file_style_selector" value="bedgraph_track_option" />
2250 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2251 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
2252 <param name="height_bedgraph" value="5" />
2253 <param name="color" value="black" />
2254 <conditional name="logScale_conditional">
2255 <param name="transform_selector" value="log2"/>
2256 <param name="log_pseudocount" value="1"/>
2257 </conditional>
2258 <param name="min_value" value="0" />
2259 <param name="show_data" value="true" />
2260 </conditional>
2261 </repeat>
2262 <repeat name="tracks">
2263 <conditional name="track_file_style_conditional">
2264 <param name="track_file_style_selector" value="bedgraph_track_option" />
2265 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2266 <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
2267 <param name="height_bedgraph" value="5" />
2268 <param name="color" value="black" />
2269 <section name="op">
2270 <param name="operation" value="log2(1+file)" />
2271 </section>
2272 <param name="min_value" value="0" />
2273 <param name="show_data" value="true" />
2274 </conditional>
2275 </repeat>
2276 <repeat name="tracks">
2277 <conditional name="track_file_style_conditional">
2278 <param name="track_file_style_selector" value="bedgraph_track_option" />
2279 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2280 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
2281 <param name="height_bedgraph" value="5" />
2282 <param name="color" value="black" />
2283 <conditional name="logScale_conditional">
2284 <param name="transform_selector" value="log2"/>
2285 <param name="log_pseudocount" value="1"/>
2286 <param name="y_axis_values" value="original"/>
2287 </conditional>
2288 <param name="min_value" value="0" />
2289 <param name="show_data" value="true" />
2290 </conditional>
2291 </repeat>
2292 <repeat name="tracks">
2293 <conditional name="track_file_style_conditional">
2294 <param name="track_file_style_selector" value="xaxis_option" />
2295 <param name="xaxis_where" value="bottom" />
2296 </conditional>
2297 </repeat>
2298 <param name="image_file_format" value="png" />
2299 <output name="outFileName" file="test_log.png" ftype="png" compare="sim_size" delta="35000" />
2300 </test>
2301 <!--test 18-->
2302 <test>
2303 <param name="region" value="chrX:2700000-3100000"/>
2304 <repeat name="tracks">
2305 <conditional name="track_file_style_conditional">
2306 <param name="track_file_style_selector" value="xaxis_option" />
2307 <param name="xaxis_where" value="top" />
2308 </conditional>
2309 </repeat>
2310 <repeat name="tracks">
2311 <conditional name="track_file_style_conditional">
2312 <param name="track_file_style_selector" value="bedgraph_track_option" />
2313 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
2314 <param name="title" value="file summary_method = mean number_of_bins=20" />
2315 <param name="height_bedgraph" value="4" />
2316 <param name="color" value="blue" />
2317 <param name="show_data" value="true" />
2318 <section name="reading_bdg_as_bw" >
2319 <param name="summary_method" value="mean" />
2320 <param name="number_of_bins" value="20" />
2321 </section>
2322 <param name="min_value" value="0" />
2323 <param name="max_value" value="30" />
2324 </conditional>
2325 </repeat>
2326 <repeat name="tracks">
2327 <conditional name="track_file_style_conditional">
2328 <param name="track_file_style_selector" value="bedgraph_track_option" />
2329 <param name="track_input_bedgraph" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
2330 <param name="title" value="second_file summary_method = mean" />
2331 <param name="height_bedgraph" value="4" />
2332 <param name="color" value="red" />
2333 <param name="show_data" value="true" />
2334 <section name="reading_bdg_as_bw" >
2335 <param name="summary_method" value="mean" />
2336 </section>
2337 <param name="min_value" value="0" />
2338 <param name="max_value" value="30" />
2339 <param name="spacer_height" value="0.5" />
2340 </conditional>
2341 </repeat>
2342 <repeat name="tracks">
2343 <conditional name="track_file_style_conditional">
2344 <param name="track_file_style_selector" value="bedgraph_track_option" />
2345 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
2346 <param name="title" value="operation = log1p(file) (no summary_method)" />
2347 <param name="height_bedgraph" value="4" />
2348 <param name="color" value="blue" />
2349 <param name="show_data" value="true" />
2350 <section name="op">
2351 <param name="operation" value="log1p(file)" />
2352 </section>
2353 <param name="spacer_height" value="0.5" />
2354 </conditional>
2355 </repeat>
2356 <repeat name="tracks">
2357 <conditional name="track_file_style_conditional">
2358 <param name="track_file_style_selector" value="bedgraph_track_option" />
2359 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
2360 <param name="title" value="operation = file - second_file" />
2361 <param name="height_bedgraph" value="8" />
2362 <param name="color" value="blue" />
2363 <param name="show_data" value="true" />
2364 <conditional name="color_negative">
2365 <param name="color_negative_select" value="true" />
2366 <param name="color" value="red" />
2367 </conditional>
2368 <section name="op">
2369 <param name="operation" value="file - second_file" />
2370 <param name="second_file" value="bedgraph2_X_2.5e6_3.5e6.bdg" ftype="bedgraph" />
2371 </section>
2372 <param name="min_value" value="-30" />
2373 <param name="max_value" value="30" />
2374 </conditional>
2375 </repeat>
2376 <param name="image_file_format" value="png" />
2377 <output name="outFileName" file="test_operation.png" ftype="png" compare="sim_size" delta="35000" />
2378 </test>
2379 <!--test 19-->
2380 <test>
2381 <param name="region" value="chr2:73,800,000-75,744,000"/>
2382 <repeat name="tracks">
2383 <conditional name="track_file_style_conditional">
2384 <param name="track_file_style_selector" value="bedgraph_track_option" />
2385 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2386 <param name="title" value="bedgraph color = blue transform = no" />
2387 <param name="height_bedgraph" value="5" />
2388 <param name="color" value="blue" />
2389 <param name="show_data" value="true" />
2390 <param name="grid" value="true" />
2391 </conditional>
2392 </repeat>
2393 <repeat name="tracks">
2394 <conditional name="track_file_style_conditional">
2395 <param name="track_file_style_selector" value="bedgraph_track_option" />
2396 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2397 <param name="title" value="bedgraph color = blue transform = log" />
2398 <param name="height_bedgraph" value="5" />
2399 <param name="color" value="blue" />
2400 <conditional name="logScale_conditional">
2401 <param name="transform_selector" value="log"/>
2402 </conditional>
2403 <param name="show_data" value="true" />
2404 <param name="grid" value="true" />
2405 </conditional>
2406 </repeat>
2407 <repeat name="tracks">
2408 <conditional name="track_file_style_conditional">
2409 <param name="track_file_style_selector" value="bedgraph_track_option" />
2410 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2411 <param name="title" value="bedgraph color = red transform = log min_value = 1" />
2412 <param name="height_bedgraph" value="5" />
2413 <param name="color" value="red" />
2414 <conditional name="logScale_conditional">
2415 <param name="transform_selector" value="log"/>
2416 </conditional>
2417 <param name="min_value" value="1" />
2418 <param name="show_data" value="true" />
2419 <param name="grid" value="true" />
2420 </conditional>
2421 </repeat>
2422 <repeat name="tracks">
2423 <conditional name="track_file_style_conditional">
2424 <param name="track_file_style_selector" value="bedgraph_track_option" />
2425 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2426 <param name="title" value="bedgraph color = green transform = log log_pseudocount = 2 min_value = 0" />
2427 <param name="height_bedgraph" value="5" />
2428 <param name="color" value="green" />
2429 <conditional name="logScale_conditional">
2430 <param name="transform_selector" value="log"/>
2431 <param name="log_pseudocount" value="2"/>
2432 </conditional>
2433 <param name="min_value" value="0" />
2434 <param name="show_data" value="true" />
2435 <param name="grid" value="true" />
2436 </conditional>
2437 </repeat>
2438 <repeat name="tracks">
2439 <conditional name="track_file_style_conditional">
2440 <param name="track_file_style_selector" value="bedgraph_track_option" />
2441 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2442 <param name="title" value="bedgraph color = green operation = log(2+file) min_value = 0.7" />
2443 <param name="height_bedgraph" value="5" />
2444 <param name="color" value="green" />
2445 <section name="op">
2446 <param name="operation" value="log(2+file)" />
2447 </section>
2448 <param name="min_value" value="0.7" />
2449 <param name="show_data" value="true" />
2450 <param name="grid" value="true" />
2451 </conditional>
2452 </repeat>
2453 <repeat name="tracks">
2454 <conditional name="track_file_style_conditional">
2455 <param name="track_file_style_selector" value="bedgraph_track_option" />
2456 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2457 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0" />
2458 <param name="height_bedgraph" value="5" />
2459 <param name="color" value="black" />
2460 <conditional name="logScale_conditional">
2461 <param name="transform_selector" value="log2"/>
2462 <param name="log_pseudocount" value="1"/>
2463 </conditional>
2464 <param name="min_value" value="0" />
2465 <param name="show_data" value="true" />
2466 <param name="grid" value="true" />
2467 </conditional>
2468 </repeat>
2469 <repeat name="tracks">
2470 <conditional name="track_file_style_conditional">
2471 <param name="track_file_style_selector" value="bedgraph_track_option" />
2472 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2473 <param name="title" value="bedgraph color = black operation = log2(1+file) min_value = 0" />
2474 <param name="height_bedgraph" value="5" />
2475 <param name="color" value="black" />
2476 <section name="op">
2477 <param name="operation" value="log2(1+file)" />
2478 </section>
2479 <param name="min_value" value="0" />
2480 <param name="show_data" value="true" />
2481 <param name="grid" value="true" />
2482 </conditional>
2483 </repeat>
2484 <repeat name="tracks">
2485 <conditional name="track_file_style_conditional">
2486 <param name="track_file_style_selector" value="bedgraph_track_option" />
2487 <param name="track_input_bedgraph" value="GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz" ftype="bedgraph" />
2488 <param name="title" value="bedgraph color = black transform = log2 log_pseudocount = 1 min_value = 0 y_axis_values = original" />
2489 <param name="height_bedgraph" value="5" />
2490 <param name="color" value="black" />
2491 <conditional name="logScale_conditional">
2492 <param name="transform_selector" value="log2"/>
2493 <param name="log_pseudocount" value="1"/>
2494 <param name="y_axis_values" value="original"/>
2495 </conditional>
2496 <param name="min_value" value="0" />
2497 <param name="show_data" value="true" />
2498 <param name="grid" value="true" />
2499 </conditional>
2500 </repeat>
2501 <repeat name="tracks">
2502 <conditional name="track_file_style_conditional">
2503 <param name="track_file_style_selector" value="xaxis_option" />
2504 <param name="xaxis_where" value="bottom" />
2505 </conditional>
2506 </repeat>
2507 <param name="image_file_format" value="png" />
2508 <output name="outFileName" file="test_log_grid.png" ftype="png" compare="sim_size" delta="35000" />
2509 </test>
2510 <!--test 20-->
2511 <test>
2512 <param name="region" value="chrX:3000000-3300000"/>
2513 <repeat name="tracks">
2514 <conditional name="track_file_style_conditional">
2515 <param name="track_file_style_selector" value="xaxis_option" />
2516 <param name="xaxis_where" value="top" />
2517 </conditional>
2518 </repeat>
2519 <repeat name="tracks">
2520 <conditional name="track_file_style_conditional">
2521 <param name="track_file_style_selector" value="spacer_option" />
2522 <param name="spacer_height" value="0.05" />
2523 </conditional>
2524 </repeat>
2525 <repeat name="tracks">
2526 <conditional name="track_file_style_conditional">
2527 <param name="track_file_style_selector" value="hic_matrix_option" />
2528 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2529 <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
2530 <param name="depth" value="300000" />
2531 <param name="transform" value="log1p" />
2532 <param name="min_value" value="5" />
2533 <param name="show_masked_bins" value="false" />
2534 </conditional>
2535 </repeat>
2536 <repeat name="tracks">
2537 <conditional name="track_file_style_conditional">
2538 <param name="track_file_style_selector" value="link_track_option" />
2539 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
2540 <conditional name="color_link">
2541 <param name="color" value="red" />
2542 </conditional>
2543 <param name="line_width" value="5" />
2544 <param name="links_type" value="loops" />
2545 <param name="overlay_select" value="share-y" />
2546 </conditional>
2547 </repeat>
2548 <repeat name="tracks">
2549 <conditional name="track_file_style_conditional">
2550 <param name="track_file_style_selector" value="link_track_option" />
2551 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
2552 <conditional name="color_link">
2553 <param name="color" value="RdYlGn" />
2554 </conditional>
2555 <param name="line_width" value="3" />
2556 <param name="invert_orientation" value="true" />
2557 <param name="title" value="links line_width = 3 color RdYlGn" />
2558 </conditional>
2559 </repeat>
2560 <repeat name="tracks">
2561 <conditional name="track_file_style_conditional">
2562 <param name="track_file_style_selector" value="spacer_option" />
2563 <param name="spacer_height" value="1" />
2564 </conditional>
2565 </repeat>
2566 <repeat name="tracks">
2567 <conditional name="track_file_style_conditional">
2568 <param name="track_file_style_selector" value="hic_matrix_option" />
2569 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
2570 <param name="title" value="depth = 300000; transform = log1p; min_value = 5 (next track: overlay_previous = share-y links_type = loops)" />
2571 <param name="depth" value="300000" />
2572 <param name="transform" value="log1p" />
2573 <param name="min_value" value="5" />
2574 <param name="show_masked_bins" value="false" />
2575 </conditional>
2576 </repeat>
2577 <repeat name="tracks">
2578 <conditional name="track_file_style_conditional">
2579 <param name="track_file_style_selector" value="link_track_option" />
2580 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
2581 <conditional name="color_link">
2582 <param name="color" value="red" />
2583 </conditional>
2584 <param name="line_width" value="5" />
2585 <param name="links_type" value="loops" />
2586 <param name="overlay_select" value="share-y" />
2587 </conditional>
2588 </repeat>
2589 <repeat name="tracks">
2590 <conditional name="track_file_style_conditional">
2591 <param name="track_file_style_selector" value="link_track_option" />
2592 <param name="track_input_link" value="test_wide.arcs" ftype="bed" />
2593 <conditional name="color_link">
2594 <param name="color" value="RdYlGn" />
2595 </conditional>
2596 <param name="line_width" value="3" />
2597 <param name="invert_orientation" value="true" />
2598 <param name="use_middle" value="true" />
2599 <param name="title" value="links line_width = 3 color RdYlGn use_middle = true" />
2600 </conditional>
2601 </repeat>
2602 <repeat name="tracks">
2603 <conditional name="track_file_style_conditional">
2604 <param name="track_file_style_selector" value="vlines_track_option" />
2605 <param name="track_input_bed_single" value="tad_classification.bed" ftype="bed" />
2606 <param name="line_width" value="3" />
2607 </conditional>
2608 </repeat>
2609 <param name="image_file_format" value="png" />
2610 <output name="outFileName" file="test_arcs_use_middle.png" ftype="png" compare="sim_size" delta="35000" />
2611 </test>
2074 </tests> 2612 </tests>
2075 <help><![CDATA[ 2613 <help><![CDATA[
2076 2614
2077 pyGenomeTracks 2615 pyGenomeTracks
2078 ============== 2616 ==============