Mercurial > repos > iuc > pygenometracks
comparison pyGenomeTracks.xml @ 8:4ac4e7083b7e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 3bfe22506f7d9922ac885ef6a6fbe8f96c83ed14"
author | iuc |
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date | Tue, 21 Jul 2020 03:32:48 -0400 |
parents | 326a3db8d9d1 |
children | 2824d77cd8f8 |
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7:326a3db8d9d1 | 8:4ac4e7083b7e |
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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 ============== |