Mercurial > repos > iuc > pygenometracks

comparison pyGenomeTracks.xml @ 4:c237ba772225 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 13ae6af8549174610888bfd8062384898c629af3"
author iuc
date Thu, 19 Sep 2019 17:18:54 -0400
parents feab9265552d
children eca03db4f612
comparison
equal deleted inserted replaced
3:feab9265552d 4:c237ba772225
1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.2"> 1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>plot genomic data tracks</description> 2 <description>plot genomic data tracks</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">pyGenomeTracks</token> 4 <token name="@BINARY@">pyGenomeTracks</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
127 color = $track.track_file_style_conditional.color 127 color = $track.track_file_style_conditional.color
128 #end if 128 #end if
129 #if $track.track_file_style_conditional.height_tad: 129 #if $track.track_file_style_conditional.height_tad:
130 height = $track.track_file_style_conditional.height_tad 130 height = $track.track_file_style_conditional.height_tad
131 #end if 131 #end if
132 #if $track.track_file_style_conditional.show_data:
133 show data range = $track.track_file_style_conditional.show_data 132 show data range = $track.track_file_style_conditional.show_data
134 #end if
135 133
136 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) 134 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
137 #if $columns > 4: 135 #if $columns > 4:
138 file_type = bedgraph_matrix 136 file_type = bedgraph_matrix
139 #if $track.track_file_style_conditional.type_lines: 137 #if $track.track_file_style_conditional.type_lines:
237 height = $track.track_file_style_conditional.spacer_height 235 height = $track.track_file_style_conditional.spacer_height
238 #end if 236 #end if
239 #end for 237 #end for
240 #end if 238 #end if
241 239
240 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option":
241 #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak):
242
243 [narrow_peak_${counter}_${counter_narrow_peak}]
244 file = $data_narrow_peak
245 #if $track.track_file_style_conditional.title:
246 title = $track.track_file_style_conditional.title
247 #else:
248 title = $data_narrow_peak.name
249 #end if
250 color = $track.track_file_style_conditional.color
251 type = $track.track_file_style_conditional.display.display_selector
252 use summit = $track.track_file_style_conditional.display.use_summit
253 #if $track.track_file_style_conditional.display.display_selector == "peak":
254 show data range = $track.track_file_style_conditional.display.show_data
255 #if $track.track_file_style_conditional.display.width_adjust:
256 width adjust = $track.track_file_style_conditional.display.width_adjust
257 #end if
258 #if $track.track_file_style_conditional.display.min_value:
259 min_value = $track.track_file_style_conditional.display.min_value
260 #end if
261 #if $track.track_file_style_conditional.display.max_value:
262 max_value = $track.track_file_style_conditional.display.max_value
263 #end if
264 #end if
265
266
267 #if $track.track_file_style_conditional.height_narrow_peak:
268 height = $track.track_file_style_conditional.height_narrow_peak
269 #end if
270
271 show labels = $track.track_file_style_conditional.show_labels
272
273 file_type = narrow_peak
274 #if $track.track_file_style_conditional.fontsize:
275 fontsize = $track.track_file_style_conditional.fontsize
276 #end if
277
278 #if $track.track_file_style_conditional.spacer_height != "":
279 [spacer]
280 height = $track.track_file_style_conditional.spacer_height
281 #end if
282 #end for
283 #end if
284
242 285
243 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": 286 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
244 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: 287 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
245 288
246 [bedgraph_$counter] 289 [bedgraph_$counter]
269 max_value = $track.track_file_style_conditional.max_value 312 max_value = $track.track_file_style_conditional.max_value
270 #else: 313 #else:
271 max_value = auto 314 max_value = auto
272 #end if 315 #end if
273 316
274 #if $track.track_file_style_conditional.show_data:
275 show data range = $track.track_file_style_conditional.show_data 317 show data range = $track.track_file_style_conditional.show_data
276 #end if
277 318
278 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) 319 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
279 #if $columns > 4: 320 #if $columns > 4:
280 file_type = bedgraph_matrix 321 file_type = bedgraph_matrix
281 type = lines 322 type = lines
337 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': 378 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
338 type = line:$track.track_file_style_conditional.type_conditional.width_line 379 type = line:$track.track_file_style_conditional.type_conditional.width_line
339 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': 380 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
340 type = points:$track.track_file_style_conditional.type_conditional.width_point 381 type = points:$track.track_file_style_conditional.type_conditional.width_point
341 #end if 382 #end if
342 #if $track.track_file_style_conditional.data_range: 383 show data range = $track.track_file_style_conditional.show_data
343 show data range = $track.track_file_style_conditional.data_range
344 #end if
345 file_type = bigwig 384 file_type = bigwig
346 #if $track.track_file_style_conditional.invert_orientation: 385 #if $track.track_file_style_conditional.invert_orientation:
347 orientation = inverted 386 orientation = inverted
348 #end if 387 #end if
349 overlay previous = $track.track_file_style_conditional.overlay_select 388 overlay previous = $track.track_file_style_conditional.overlay_select
428 <param name="track_file_style_selector" type="select" label="Choose style of the track"> 467 <param name="track_file_style_selector" type="select" label="Choose style of the track">
429 <option value="hic_matrix_option">TAD visualization</option> 468 <option value="hic_matrix_option">TAD visualization</option>
430 <option value="chrom_states_option">Chromatine states</option> 469 <option value="chrom_states_option">Chromatine states</option>
431 <option value="tad_score_track_option">TAD score</option> 470 <option value="tad_score_track_option">TAD score</option>
432 <option value="gene_track_option">Gene track / Bed track</option> 471 <option value="gene_track_option">Gene track / Bed track</option>
472 <option value="narrow_peak_track_option">NarrowPeak track</option>
433 <option value="bigwig_track_option">Bigwig track</option> 473 <option value="bigwig_track_option">Bigwig track</option>
434 <option value="bedgraph_track_option">Bedgraph track </option> 474 <option value="bedgraph_track_option">Bedgraph track </option>
435 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> 475 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
436 <option value="vlines_track_option">Vlines track</option> 476 <option value="vlines_track_option">Vlines track</option>
437 <option value="spacer_option">Spacer</option> 477 <option value="spacer_option">Spacer</option>
465 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 505 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
466 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" 506 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
467 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead 507 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
468 of the matrix set to lines if a heatmap representing the matrix is not wanted"/> 508 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
469 <param name="height_tad" type="float" value="0.2" optional="True" label="height"/> 509 <param name="height_tad" type="float" value="0.2" optional="True" label="height"/>
470 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> 510 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" />
471 <expand macro="spacer_macro" /> 511 <expand macro="spacer_macro" />
472 512
473 </when> 513 </when>
474 <when value="chrom_states_option"> 514 <when value="chrom_states_option">
475 <expand macro="plot_title" /> 515 <expand macro="plot_title" />
502 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> 542 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
503 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 543 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
504 <expand macro="spacer_macro" /> 544 <expand macro="spacer_macro" />
505 545
506 </when> 546 </when>
547 <when value="narrow_peak_track_option">
548 <expand macro="plot_title" />
549 <expand macro="track_input_narrow_peak_macro" />
550 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
551 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/>
552 <conditional name="display">
553 <param name="display_selector" type="select" label="display to use">
554 <option value="peak" selected="True">peak: Draw a peak shape from start, end, summit, height</option>
555 <option value="box">box: Draw a box</option>
556 </param>
557 <when value="peak">
558 <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true"
559 optional="True" label="Use summit information to make the curve." />
560 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false"
561 label="Show visualization of data range" />
562 <param name='width_adjust' type="float" value="1.5" optional="True"
563 label="Factor to change the width of the curve."/>
564 <expand macro="minmax_macro" />
565 </when>
566 <when value="box">
567 <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true"
568 optional="True" label="Plot a vertical bar at the summit position." />
569 </when>
570 </conditional>
571 <param name="show_labels" type="boolean" truevalue="yes" falsevalue="no" checked="true"
572 label="Plot labels (name, p-val, q-val)" />
573 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
574 <expand macro="spacer_macro" />
575
576 </when>
507 <when value="bedgraph_track_option"> 577 <when value="bedgraph_track_option">
508 <expand macro="plot_title" /> 578 <expand macro="plot_title" />
509 <expand macro="track_input_bedgraph_macro" /> 579 <expand macro="track_input_bedgraph_macro" />
510 <expand macro="color_coverage_macro" /> 580 <expand macro="color_coverage_macro" />
511 <expand macro="minmax_macro" /> 581 <expand macro="minmax_macro" />
512 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> 582 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
513 <expand macro="type_coverage_macro" /> 583 <expand macro="type_coverage_macro" />
514 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" /> 584 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" />
515 <expand macro="inverted_macro" /> 585 <expand macro="inverted_macro" />
516 <expand macro="overlay_macro" /> 586 <expand macro="overlay_macro" />
517 <expand macro="spacer_macro" /> 587 <expand macro="spacer_macro" />
518 588
519 </when> 589 </when>
527 597
528 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> 598 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
529 <expand macro="reading_bw_macro" /> 599 <expand macro="reading_bw_macro" />
530 <expand macro="type_coverage_macro" /> 600 <expand macro="type_coverage_macro" />
531 <expand macro="type_coverage_macro" /> 601 <expand macro="type_coverage_macro" />
532 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" label="Show visualization of data range"/> 602 <param name="show_data" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range"/>
533 <expand macro="inverted_macro" /> 603 <expand macro="inverted_macro" />
534 <expand macro="overlay_macro" /> 604 <expand macro="overlay_macro" />
535 <expand macro="spacer_macro" /> 605 <expand macro="spacer_macro" />
536 606
537 </when> 607 </when>
967 <param name="track_file_style_selector" value="bigwig_track_option" /> 1037 <param name="track_file_style_selector" value="bigwig_track_option" />
968 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 1038 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
969 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" /> 1039 <param name="title" value="(bigwig color=blue 2000 bins) overlayed with (bigwig mean color=red alpha = 0.5 max over 300 bins)" />
970 <param name="height_bigwig" value="7" /> 1040 <param name="height_bigwig" value="7" />
971 <param name="color" value="#00b0f0" /> 1041 <param name="color" value="#00b0f0" />
972 <param name="number_of_bins" value="2000"/> 1042 <section name="reading_bw_conditional">
1043 <param name="number_of_bins" value="2000"/>
1044 </section>
973 </conditional> 1045 </conditional>
974 </repeat> 1046 </repeat>
975 <repeat name="tracks"> 1047 <repeat name="tracks">
976 <conditional name="track_file_style_conditional"> 1048 <conditional name="track_file_style_conditional">
977 <param name="track_file_style_selector" value="bigwig_track_option" /> 1049 <param name="track_file_style_selector" value="bigwig_track_option" />
978 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 1050 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
979 <param name="title" value="" /> 1051 <param name="title" value="" />
980 <param name="color" value="#ff0000" /> 1052 <param name="color" value="#ff0000" />
981 <param name="alpha" value="0.5" /> 1053 <param name="alpha" value="0.5" />
982 <param name="summary" value="max" /> 1054 <param name="summary" value="max" />
983 <param name="number_of_bins" value="300"/> 1055 <section name="reading_bw_conditional">
1056 <param name="number_of_bins" value="300"/>
1057 </section>
984 <param name="overlay_select" value="share-y"/> 1058 <param name="overlay_select" value="share-y"/>
985 </conditional> 1059 </conditional>
986 </repeat> 1060 </repeat>
987 <param name="image_file_format" value="png" /> 1061 <param name="image_file_format" value="png" />
988 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> 1062 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" />
1014 <param name="spacer_height" value="1"/> 1088 <param name="spacer_height" value="1"/>
1015 </conditional> 1089 </conditional>
1016 </repeat> 1090 </repeat>
1017 <param name="image_file_format" value="png" /> 1091 <param name="image_file_format" value="png" />
1018 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> 1092 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />
1093 </test>
1094 <test>
1095 <param name="region" value="X:2760000-2802000"/>
1096 <conditional name="x_axis">
1097 <param name="x_axis_select" value="yes" />
1098 <param name="where" value="bottom" />
1099 </conditional>
1100 <repeat name="tracks">
1101 <conditional name="track_file_style_conditional">
1102 <param name="track_file_style_selector" value="narrow_peak_track_option" />
1103 <param name="title" value="box" />
1104 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
1105 <param name="color" value="#9bbb59" />
1106 <param name="height_narrow_peak" value="4" />
1107 <conditional name="display">
1108 <param name="display_selector" value="box" />
1109 <param name="use_summit" value="yes" />
1110 </conditional>
1111 <param name="show_labels" value="yes" />
1112 </conditional>
1113 </repeat>
1114 <repeat name="tracks">
1115 <conditional name="track_file_style_conditional">
1116 <param name="track_file_style_selector" value="narrow_peak_track_option" />
1117 <param name="title" value="peak width 3" />
1118 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
1119 <param name="color" value="#c0504d" />
1120 <param name="height_narrow_peak" value="4" />
1121 <conditional name="display">
1122 <param name="display_selector" value="peak" />
1123 <param name="use_summit" value="yes" />
1124 <param name="show_data" value="yes" />
1125 <param name="width_adjust" value="3" />
1126 <param name="max_value" value="50" />
1127 </conditional>
1128 <param name="show_labels" value="no" />
1129 <param name="spacer_height" value="0.5"/>
1130 </conditional>
1131 </repeat>
1132 <repeat name="tracks">
1133 <conditional name="track_file_style_conditional">
1134 <param name="track_file_style_selector" value="narrow_peak_track_option" />
1135 <param name="title" value="peak no data range" />
1136 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
1137 <param name="color" value="#000000" />
1138 <param name="height_narrow_peak" value="4" />
1139 <conditional name="display">
1140 <param name="display_selector" value="peak" />
1141 <param name="use_summit" value="no" />
1142 <param name="show_data" value="no" />
1143 </conditional>
1144 <param name="show_labels" value="yes" />
1145 </conditional>
1146 </repeat>
1147 <param name="image_file_format" value="png" />
1148 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" />
1019 </test> 1149 </test>
1020 </tests> 1150 </tests>
1021 <help><![CDATA[ 1151 <help><![CDATA[
1022 1152
1023 pyGenomeTracks 1153 pyGenomeTracks