Mercurial > repos > iuc > pygenometracks

comparison pyGenomeTracks.xml @ 5:eca03db4f612 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
author iuc
date Wed, 08 Jan 2020 09:15:19 -0500
parents c237ba772225
children 5cec5fb749f0
comparison
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4:c237ba772225 5:eca03db4f612
1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@.1"> 1 <tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@">
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>
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 #for $counter, $track in enumerate($tracks): 11 #for $counter, $track in enumerate($tracks):
11 #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":
12 #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):
13 #set ext = $data_matrix.extension 14 #set ext = $data_matrix.extension
14 ln -s $data_matrix ${counter}_${counter_matrix}.$ext && 15 ln -s $data_matrix ${counter}_${counter_matrix}.$ext &&
33 && mv plot.$image_file_format plot 34 && mv plot.$image_file_format plot
34 ]]> 35 ]]>
35 </command> 36 </command>
36 <configfiles> 37 <configfiles>
37 <configfile name="tracks_config"> 38 <configfile name="tracks_config">
38 #if $x_axis.x_axis_select == "yes": 39 ## First the xaxis if where = top
39 #if $x_axis.where == 'top': 40 #if $x_axis.x_axis_select == "true":
41 #if $x_axis.where == 'top':
40 [x-axis] 42 [x-axis]
41 #if $x_axis.fontsize: 43 #if $x_axis.fontsize:
42 fontsize = $x_axis.fontsize 44 fontsize = $x_axis.fontsize
45 #end if
46 where = top
47 #end if
43 #end if 48 #end if
44 #if $x_axis.where: 49
45 where = $x_axis.where 50 ## Then each track:
46 #end if
47 #end if
48 #end if
49 #for $counter, $track in enumerate($tracks): 51 #for $counter, $track in enumerate($tracks):
50 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option": 52 ## Hi-C Track
51 53 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
52 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple): 54 #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
53 [hic_section_${counter}_${counter_matrix}] 55 [hic_section_${counter}_${counter_matrix}]
54 #set ext = $data_matrix.extension 56 #set ext = $data_matrix.extension
55 file = ${counter}_${counter_matrix}.$ext 57 file = ${counter}_${counter_matrix}.$ext
56 file_type = hic_matrix 58 file_type = hic_matrix
57 #if $track.track_file_style_conditional.title: 59 #if $track.track_file_style_conditional.title:
58 title = $track.track_file_style_conditional.title 60 title = $track.track_file_style_conditional.title
59 #else: 61 #else:
60 title = $data_matrix.name 62 title = $data_matrix.name
61 #end if 63 #end if
62 #if $track.track_file_style_conditional.depth: 64 #if $track.track_file_style_conditional.depth:
63 depth = $track.track_file_style_conditional.depth 65 depth = $track.track_file_style_conditional.depth
64 #end if 66 #end if
65 #if $track.track_file_style_conditional.colormap: 67 #if $track.track_file_style_conditional.colormap:
66 colormap = $track.track_file_style_conditional.colormap 68 colormap = $track.track_file_style_conditional.colormap
67 #end if 69 #end if
68 #if $track.track_file_style_conditional.min_value: 70 #if $track.track_file_style_conditional.min_value:
69 min_value = $track.track_file_style_conditional.min_value 71 min_value = $track.track_file_style_conditional.min_value
70 #end if 72 #end if
71 #if $track.track_file_style_conditional.max_value: 73 #if $track.track_file_style_conditional.max_value:
72 max_value = $track.track_file_style_conditional.max_value 74 max_value = $track.track_file_style_conditional.max_value
73 #end if 75 #end if
74 #if $track.track_file_style_conditional.transform != "":
75 transform = $track.track_file_style_conditional.transform 76 transform = $track.track_file_style_conditional.transform
76 #end if 77 #if $track.track_file_style_conditional.height_matrix != "":
77 #if $track.track_file_style_conditional.height_matrix != "":
78 height = $track.track_file_style_conditional.height_matrix 78 height = $track.track_file_style_conditional.height_matrix
79 #end if 79 #end if
80 80 #if $track.track_file_style_conditional.show_masked_bins:
81 #if $track.track_file_style_conditional.show_masked_bins:
82 show_masked_bins = $track.track_file_style_conditional.show_masked_bins 81 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
83 #end if 82 #end if
84 #if $track.track_file_style_conditional.invert_orientation: 83 #if $track.track_file_style_conditional.invert_orientation:
85 orientation = inverted 84 orientation = inverted
86 #end if 85 #end if
87 #if $track.track_file_style_conditional.scale_factor: 86 #if $track.track_file_style_conditional.scale_factor:
88 scale factor = $track.track_file_style_conditional.scale_factor 87 scale_factor = $track.track_file_style_conditional.scale_factor
89 #end if 88 #end if
90 89 rasterize = $track.track_file_style_conditional.rasterize
91 #if str($track.track_file_style_conditional.boundaries_file) != "None": 90 ## If a boundary file is given a new section needs to be written:
92 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix: 91 #if str($track.track_file_style_conditional.boundaries_file) != "None":
93 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix] 92 #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
94 #else: 93 #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
95 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0] 94 #else:
96 #end if 95 #set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
96 #end if
97 [tads_${counter}_${counter_matrix}] 97 [tads_${counter}_${counter_matrix}]
98 file = $boundary_file 98 file = $boundary_file
99 file_type = domains 99 file_type = domains
100 border color = black 100 border_color = black
101 color = none 101 color = none
102 overlay previous = share-y 102 overlay_previous = share-y
103 #end if 103 #end if
104 104 ## If spacer is asked a new section is created:
105 105 #if $track.track_file_style_conditional.spacer_height != "":
106 #if $track.track_file_style_conditional.spacer_height != "":
107 [spacer] 106 [spacer]
108 height = $track.track_file_style_conditional.spacer_height 107 height = $track.track_file_style_conditional.spacer_height
109 #end if 108 #end if
110 #end for 109 #end for
111 110 #end if
112 #end if 111
113 112 ## Chrom_state track
114 113 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
115 114 #for $data_bed in $track.track_file_style_conditional.track_input_bed:
116 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option": 115 [chrom states_$counter]
117 116 file = $data_bed
118 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: 117 #if $track.track_file_style_conditional.title:
119 [tad_score_$counter]
120 file = $data_bedgraph
121 #if $track.track_file_style_conditional.title:
122 title = $track.track_file_style_conditional.title 118 title = $track.track_file_style_conditional.title
123 #else: 119 #else:
124 title = $data_bedgraph.name 120 title = $data_bed.name
125 #end if 121 #end if
126 #if $track.track_file_style_conditional.color: 122 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
127 color = $track.track_file_style_conditional.color 123 color = bed_rgb
128 #end if 124 #elif $track.track_file_style_conditional.color_bed.color:
129 #if $track.track_file_style_conditional.height_tad: 125 color = $track.track_file_style_conditional.color_bed.color
130 height = $track.track_file_style_conditional.height_tad 126 #end if
131 #end if 127 #if $track.track_file_style_conditional.border_color:
132 show data range = $track.track_file_style_conditional.show_data 128 border_color = $track.track_file_style_conditional.border_color
133 129 #end if
134 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t')) 130 display = collapsed
135 #if $columns > 4: 131 #if $track.track_file_style_conditional.height_chrom:
136 file_type = bedgraph_matrix 132 height = $track.track_file_style_conditional.height_chrom
137 #if $track.track_file_style_conditional.type_lines: 133 #end if
138 type = $track.track_file_style_conditional.type_lines 134 line_width = $track.track_file_style_conditional.line_width
139 #end if 135 file_type = bed
140 #else: 136 ## If spacer is asked a new section is created:
141 file_type = bedgraph 137 #if $track.track_file_style_conditional.spacer_height != "":
142 #end if
143 #if $track.track_file_style_conditional.spacer_height != "":
144 [spacer] 138 [spacer]
145 height = $track.track_file_style_conditional.spacer_height 139 height = $track.track_file_style_conditional.spacer_height
146 #end if 140 #end if
147 #end for 141 #end for
148 #end if 142 #end if
149 143
150 144 ## Gene/gtf track
151 145 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
152 146 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
153 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option": 147 [genes_${counter}_${counter_bed}]
154 #for $data_bed in $track.track_file_style_conditional.track_input_bed: 148 #set ext = $data_bed.extension
155 149 file = ${counter}_${counter_bed}.$ext
156 [chrom states_$counter] 150 #if $ext == 'gtf':
157 file = $data_bed 151 prefered_name = $track.track_file_style_conditional.bed_advanced.gtf.prefered_name
158 #if $track.track_file_style_conditional.title: 152 merge_transcripts = $track.track_file_style_conditional.bed_advanced.gtf.merge_transcripts
153 #end if
154 #if $track.track_file_style_conditional.title:
159 title = $track.track_file_style_conditional.title 155 title = $track.track_file_style_conditional.title
160 #else: 156 #elif $track.track_file_style_conditional.overlay_select == 'no':
161 title = $data_bed.name 157 title = $data_bed.name
162 #end if 158 #end if
163 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": 159 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
164 color = bed_rgb 160 color = bed_rgb
165 #elif $track.track_file_style_conditional.color_bed.color: 161 #elif $track.track_file_style_conditional.color_bed.color:
166 color = $track.track_file_style_conditional.color_bed.color 162 color = $track.track_file_style_conditional.color_bed.color
167 #end if 163 #end if
168 #if $track.track_file_style_conditional.border_color: 164 #if $track.track_file_style_conditional.border_color:
169 border color = $track.track_file_style_conditional.border_color 165 border_color = $track.track_file_style_conditional.border_color
170 #end if 166 #end if
171 display = collapsed 167 #if $track.track_file_style_conditional.flybase:
172 #if $track.track_file_style_conditional.height_chrom: 168 style = flybase
173 height = $track.track_file_style_conditional.height_chrom 169 height_utr = $track.track_file_style_conditional.bed_advanced.flybase.height_utr
174 #end if 170 color_utr = $track.track_file_style_conditional.bed_advanced.flybase.color_utr
171 #else
172 style = UCSC
173 arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval
174 #end if
175 display = $track.track_file_style_conditional.display
176 #if $track.track_file_style_conditional.height_bed:
177 height = $track.track_file_style_conditional.height_bed
178 #end if
179 labels = $track.track_file_style_conditional.labels
175 file_type = bed 180 file_type = bed
176 #if $track.track_file_style_conditional.spacer_height != "": 181 #if $track.track_file_style_conditional.fontsize:
182 fontsize = $track.track_file_style_conditional.fontsize
183 #end if
184 #if $track.track_file_style_conditional.bed_advanced.gene_rows:
185 gene_rows = $track.track_file_style_conditional.bed_advanced.gene_rows
186 #end if
187 global_max_row = $track.track_file_style_conditional.bed_advanced.global_max_row
188 max_labels = $track.track_file_style_conditional.bed_advanced.max_labels
189 line_width = $track.track_file_style_conditional.bed_advanced.line_width
190 arrowhead_included = $track.track_file_style_conditional.arrowhead_included
191 #if $track.track_file_style_conditional.invert_orientation:
192 orientation = inverted
193 #end if
194 overlay_previous = $track.track_file_style_conditional.overlay_select
195 ## If spacer is asked a new section is created:
196 #if $track.track_file_style_conditional.spacer_height != "":
177 [spacer] 197 [spacer]
178 height = $track.track_file_style_conditional.spacer_height 198 height = $track.track_file_style_conditional.spacer_height
179 #end if 199 #end if
180 #end for 200 #end for
181 201 #end if
182 #end if 202
183 203 ## Link
184 204 #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option":
185 205 [links_$counter]
186 206 file = $track.track_file_style_conditional.track_input_link
187 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option": 207 #if $track.track_file_style_conditional.title:
188 #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
189
190 [genes_${counter}_${counter_bed}]
191 #set ext = $data_bed.extension
192 file = ${counter}_${counter_bed}.$ext
193 #if $track.track_file_style_conditional.title:
194 title = $track.track_file_style_conditional.title 208 title = $track.track_file_style_conditional.title
195 #else: 209 #elif $track.track_file_style_conditional.overlay_select == 'no':
196 title = $data_bed.name 210 title = $track.track_file_style_conditional.track_input_link.name
197 #end if 211 #end if
198 #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": 212 #if $track.track_file_style_conditional.height:
199 color = bed_rgb 213 height = $track.track_file_style_conditional.height
200 #elif $track.track_file_style_conditional.color_bed.color: 214 #end if
201 color = $track.track_file_style_conditional.color_bed.color 215 #if $track.track_file_style_conditional.min_value:
202 #end if 216 min_value = $track.track_file_style_conditional.min_value
203 #if $track.track_file_style_conditional.border_color: 217 #end if
204 border color = $track.track_file_style_conditional.border_color 218 #if $track.track_file_style_conditional.max_value:
205 #end if 219 max_value = $track.track_file_style_conditional.max_value
206 220 #end if
207 #if $track.track_file_style_conditional.flybase: 221 color = $track.track_file_style_conditional.color_link.color
208 style = flybase 222 alpha = $track.track_file_style_conditional.alpha
209 #else 223 line_width = $track.track_file_style_conditional.line_width
210 style = UCSC 224 line_style = $track.track_file_style_conditional.line_style
211 #end if 225 links_type = $track.track_file_style_conditional.links_type
212 226 #if $track.track_file_style_conditional.invert_orientation:
213 display = $track.track_file_style_conditional.display 227 orientation = inverted
214 228 #end if
215 #if $track.track_file_style_conditional.height_bed: 229 overlay_previous = $track.track_file_style_conditional.overlay_select
216 height = $track.track_file_style_conditional.height_bed 230 file_type = links
217 #end if 231 ## If spacer is asked a new section is created:
218 232 #if $track.track_file_style_conditional.spacer_height != "":
219 labels = $track.track_file_style_conditional.labels
220
221 file_type = bed
222 #if $track.track_file_style_conditional.fontsize:
223 fontsize = $track.track_file_style_conditional.fontsize
224 #end if
225
226 #if $track.track_file_style_conditional.gene_rows:
227 gene rows = $track.track_file_style_conditional.gene_rows
228 #end if
229
230 #if $track.track_file_style_conditional.global_max_row:
231 global max row = $track.track_file_style_conditional.global_max_row
232 #end if
233 #if $track.track_file_style_conditional.spacer_height != "":
234 [spacer] 233 [spacer]
235 height = $track.track_file_style_conditional.spacer_height 234 height = $track.track_file_style_conditional.spacer_height
236 #end if 235 #end if
237 #end for 236 #end if
238 #end if 237
239 238 ## Narrow peak
240 #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option": 239 #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): 240 #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}] 241 [narrow_peak_${counter}_${counter_narrow_peak}]
244 file = $data_narrow_peak 242 file = $data_narrow_peak
245 #if $track.track_file_style_conditional.title: 243 #if $track.track_file_style_conditional.title:
246 title = $track.track_file_style_conditional.title 244 title = $track.track_file_style_conditional.title
247 #else: 245 #elif $track.track_file_style_conditional.overlay_select == 'no':
248 title = $data_narrow_peak.name 246 title = $data_narrow_peak.name
249 #end if 247 #end if
250 color = $track.track_file_style_conditional.color 248 color = $track.track_file_style_conditional.color
251 type = $track.track_file_style_conditional.display.display_selector 249 type = $track.track_file_style_conditional.display.display_selector
252 use summit = $track.track_file_style_conditional.display.use_summit 250 use_summit = $track.track_file_style_conditional.display.use_summit
253 #if $track.track_file_style_conditional.display.display_selector == "peak": 251 #if $track.track_file_style_conditional.display.display_selector == "peak":
254 show data range = $track.track_file_style_conditional.display.show_data 252 show_data_range = $track.track_file_style_conditional.display.show_data
255 #if $track.track_file_style_conditional.display.width_adjust: 253 #if $track.track_file_style_conditional.display.width_adjust:
256 width adjust = $track.track_file_style_conditional.display.width_adjust 254 width_adjust = $track.track_file_style_conditional.display.width_adjust
257 #end if 255 #end if
258 #if $track.track_file_style_conditional.display.min_value: 256 #if $track.track_file_style_conditional.display.min_value:
259 min_value = $track.track_file_style_conditional.display.min_value 257 min_value = $track.track_file_style_conditional.display.min_value
260 #end if 258 #end if
261 #if $track.track_file_style_conditional.display.max_value: 259 #if $track.track_file_style_conditional.display.max_value:
262 max_value = $track.track_file_style_conditional.display.max_value 260 max_value = $track.track_file_style_conditional.display.max_value
263 #end if 261 #end if
264 #end if 262 #end if
265 263 #if $track.track_file_style_conditional.height_narrow_peak:
266
267 #if $track.track_file_style_conditional.height_narrow_peak:
268 height = $track.track_file_style_conditional.height_narrow_peak 264 height = $track.track_file_style_conditional.height_narrow_peak
269 #end if 265 #end if
270 266 show_labels = $track.track_file_style_conditional.show_labels
271 show labels = $track.track_file_style_conditional.show_labels
272
273 file_type = narrow_peak 267 file_type = narrow_peak
274 #if $track.track_file_style_conditional.fontsize: 268 #if $track.track_file_style_conditional.fontsize:
275 fontsize = $track.track_file_style_conditional.fontsize 269 fontsize = $track.track_file_style_conditional.fontsize
276 #end if 270 #end if
277 271 #if $track.track_file_style_conditional.invert_orientation:
278 #if $track.track_file_style_conditional.spacer_height != "": 272 orientation = inverted
273 #end if
274 overlay_previous = $track.track_file_style_conditional.overlay_select
275 ## If spacer is asked a new section is created:
276 #if $track.track_file_style_conditional.spacer_height != "":
279 [spacer] 277 [spacer]
280 height = $track.track_file_style_conditional.spacer_height 278 height = $track.track_file_style_conditional.spacer_height
281 #end if 279 #end if
282 #end for 280 #end for
283 #end if 281 #end if
284 282
285 283 ## Bedgraph track
286 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option": 284 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
287 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph: 285 #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
288
289 [bedgraph_$counter] 286 [bedgraph_$counter]
290 file = $data_bedgraph 287 file = $data_bedgraph
291 #if $track.track_file_style_conditional.title: 288 #if $track.track_file_style_conditional.title:
292 title = $track.track_file_style_conditional.title 289 title = $track.track_file_style_conditional.title
293 #elif $track.track_file_style_conditional.overlay_select == "no": 290 #elif $track.track_file_style_conditional.overlay_select == "no":
294 title = $data_bedgraph.name 291 title = $data_bedgraph.name
295 #end if 292 #end if
296 #if $track.track_file_style_conditional.color: 293 #if $track.track_file_style_conditional.color:
297 color = $track.track_file_style_conditional.color 294 color = $track.track_file_style_conditional.color
298 #end if 295 #end if
299 alpha = $track.track_file_style_conditional.alpha 296 alpha = $track.track_file_style_conditional.alpha
300 #if $track.track_file_style_conditional.color_negative.color_negative_select == "yes": 297 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
301 negative color = $track.track_file_style_conditional.color_negative.color 298 negative_color = $track.track_file_style_conditional.color_negative.color
302 #end if 299 #end if
303 #if $track.track_file_style_conditional.height_bedgraph: 300 #if $track.track_file_style_conditional.height_bedgraph:
304 height = $track.track_file_style_conditional.height_bedgraph 301 height = $track.track_file_style_conditional.height_bedgraph
305 #end if 302 #end if
306 #if $track.track_file_style_conditional.min_value: 303 #if $track.track_file_style_conditional.min_value:
307 min_value = $track.track_file_style_conditional.min_value 304 min_value = $track.track_file_style_conditional.min_value
308 #else: 305 #end if
309 min_value = auto 306 #if $track.track_file_style_conditional.max_value:
310 #end if
311 #if $track.track_file_style_conditional.max_value:
312 max_value = $track.track_file_style_conditional.max_value 307 max_value = $track.track_file_style_conditional.max_value
313 #else: 308 #end if
314 max_value = auto 309 show_data_range = $track.track_file_style_conditional.show_data
315 #end if 310 nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros
316 311 use_middle = $track.track_file_style_conditional.use_middle
317 show data range = $track.track_file_style_conditional.show_data 312 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
318 313 #if $columns > 4:
319 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
320 #if $columns > 4:
321 file_type = bedgraph_matrix 314 file_type = bedgraph_matrix
322 type = lines 315 type = lines
323 #else: 316 #else:
324 file_type = bedgraph 317 file_type = bedgraph
325 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': 318 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
326 type = fill 319 type = fill
327 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': 320 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
328 type = line:$track.track_file_style_conditional.type_conditional.width_line 321 type = line:$track.track_file_style_conditional.type_conditional.width_line
329 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': 322 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
330 type = points:$track.track_file_style_conditional.type_conditional.width_point 323 type = points:$track.track_file_style_conditional.type_conditional.width_point
331 #end if 324 #end if
332 #end if 325 #end if
333 #if $track.track_file_style_conditional.invert_orientation: 326 #if $track.track_file_style_conditional.invert_orientation:
334 orientation = inverted 327 orientation = inverted
335 #end if 328 #end if
336 overlay previous = $track.track_file_style_conditional.overlay_select 329 overlay_previous = $track.track_file_style_conditional.overlay_select
337 #if $track.track_file_style_conditional.spacer_height != "": 330 ## If spacer is asked a new section is created:
331 #if $track.track_file_style_conditional.spacer_height != "":
338 [spacer] 332 [spacer]
339 height = $track.track_file_style_conditional.spacer_height 333 height = $track.track_file_style_conditional.spacer_height
340 #end if 334 #end if
341 #end for 335 #end for
342 #end if 336 #end if
343 337
344 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option": 338 ## Bigwig tracks
345 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig: 339 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
340 #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
346 [bigwig_$counter] 341 [bigwig_$counter]
347 file = $data_bigwig 342 file = $data_bigwig
348 #if $track.track_file_style_conditional.title: 343 #if $track.track_file_style_conditional.title:
349 title = $track.track_file_style_conditional.title 344 title = $track.track_file_style_conditional.title
350 #elif $track.track_file_style_conditional.overlay_select == "no": 345 #elif $track.track_file_style_conditional.overlay_select == "no":
351 title = $data_bigwig.name 346 title = $data_bigwig.name
352 #end if 347 #end if
353 #if $track.track_file_style_conditional.color: 348 #if $track.track_file_style_conditional.color:
354 color = $track.track_file_style_conditional.color 349 color = $track.track_file_style_conditional.color
355 #end if 350 #end if
356 alpha = $track.track_file_style_conditional.alpha 351 alpha = $track.track_file_style_conditional.alpha
357 #if $track.track_file_style_conditional.color_negative.color_negative_select == "yes": 352 #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
358 negative color = $track.track_file_style_conditional.color_negative.color 353 negative_color = $track.track_file_style_conditional.color_negative.color
359 #end if 354 #end if
360 #if $track.track_file_style_conditional.min_value: 355 #if $track.track_file_style_conditional.min_value:
361 min_value = $track.track_file_style_conditional.min_value 356 min_value = $track.track_file_style_conditional.min_value
362 #else: 357 #end if
363 min_value = 0 358 #if $track.track_file_style_conditional.max_value:
364 #end if
365 #if $track.track_file_style_conditional.max_value:
366 max_value = $track.track_file_style_conditional.max_value 359 max_value = $track.track_file_style_conditional.max_value
367 #else: 360 #end if
368 max_value = auto
369 #end if
370 height = $track.track_file_style_conditional.height_bigwig 361 height = $track.track_file_style_conditional.height_bigwig
371 summary method = $track.track_file_style_conditional.reading_bw_conditional.summary 362 summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary
372 nans to zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros 363 nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
373 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins: 364 #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
374 number of bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins 365 number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
375 #end if 366 #end if
376 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option': 367 #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
377 type = fill 368 type = fill
378 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option': 369 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
379 type = line:$track.track_file_style_conditional.type_conditional.width_line 370 type = line:$track.track_file_style_conditional.type_conditional.width_line
380 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option': 371 #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
381 type = points:$track.track_file_style_conditional.type_conditional.width_point 372 type = points:$track.track_file_style_conditional.type_conditional.width_point
382 #end if 373 #end if
383 show data range = $track.track_file_style_conditional.show_data 374 show_data_range = $track.track_file_style_conditional.show_data
384 file_type = bigwig 375 file_type = bigwig
385 #if $track.track_file_style_conditional.invert_orientation: 376 #if $track.track_file_style_conditional.invert_orientation:
386 orientation = inverted 377 orientation = inverted
387 #end if 378 #end if
388 overlay previous = $track.track_file_style_conditional.overlay_select 379 overlay_previous = $track.track_file_style_conditional.overlay_select
389 #if $track.track_file_style_conditional.spacer_height != "": 380 ## If spacer is asked a new section is created:
381 #if $track.track_file_style_conditional.spacer_height != "":
390 [spacer] 382 [spacer]
391 height = $track.track_file_style_conditional.spacer_height 383 height = $track.track_file_style_conditional.spacer_height
392 #end if 384 #end if
393 #end for 385 #end for
394 #end if 386 #end if
395 387
396 388 ## bedgraph_matrix
397 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option": 389 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
398 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix: 390 #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
399
400 [bedgraph_matrix_$counter] 391 [bedgraph_matrix_$counter]
401 file = $data_bedgraph_matrix 392 file = $data_bedgraph_matrix
402 #if $track.track_file_style_conditional.title: 393 #if $track.track_file_style_conditional.title:
403 title = $track.track_file_style_conditional.title 394 title = $track.track_file_style_conditional.title
404 #else: 395 #else:
405 title = $data_bedgraph_matrix.name 396 title = $data_bedgraph_matrix.name
406 #end if 397 #end if
407 #if $track.track_file_style_conditional.height_bedgraph: 398 #if $track.track_file_style_conditional.height_bedgraph:
408 height = $track.track_file_style_conditional.height_bedgraph 399 height = $track.track_file_style_conditional.height_bedgraph
409 #end if 400 #end if
401 #if $track.track_file_style_conditional.min_value:
402 min_value = $track.track_file_style_conditional.min_value
403 #end if
404 #if $track.track_file_style_conditional.max_value:
405 max_value = $track.track_file_style_conditional.max_value
406 #end if
407 #if $track.track_file_style_conditional.type_lines:
408 type = $track.track_file_style_conditional.type_lines
409 #end if
410 file_type = bedgraph_matrix
411 show_data_range = $track.track_file_style_conditional.show_data
412 plot_horizontal_lines = $track.track_file_style_conditional.plot_horizontal_lines
413 pos_score_in_bin = $track.track_file_style_conditional.pos_score_in_bin
414 #if $track.track_file_style_conditional.invert_orientation:
410 orientation = inverted 415 orientation = inverted
411 #if $track.track_file_style_conditional.min_value: 416 #end if
412 min_value = $track.track_file_style_conditional.min_value 417 ## If spacer is asked a new section is created:
413 #end if 418 #if $track.track_file_style_conditional.spacer_height != "":
414 #if $track.track_file_style_conditional.max_value:
415 max_value = $track.track_file_style_conditional.max_value
416 #end if
417 #if $track.track_file_style_conditional.type_lines:
418 type = $track.track_file_style_conditional.type_lines
419 #end if
420 file_type = bedgraph_matrix
421 plot horizontal lines=False
422 #if $track.track_file_style_conditional.invert_orientation:
423 orientation = inverted
424 #end if
425 #if $track.track_file_style_conditional.spacer_height != "":
426 [spacer] 419 [spacer]
427 height = $track.track_file_style_conditional.spacer_height 420 height = $track.track_file_style_conditional.spacer_height
428 #end if 421 #end if
429 #end for 422 #end for
430 #end if 423 #end if
431 424
432 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option": 425 ## Vlines:
433 426 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
434 [vlines_$counter] 427 [vlines_$counter]
435 file = $track.track_file_style_conditional.track_input_bed_single 428 file = $track.track_file_style_conditional.track_input_bed_single
436 type = vlines 429 type = vlines
437 file_type = bed 430 #end if
438 #end if 431
439 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option": 432 ## Hlines:
440 433 #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option":
441 #if $track.track_file_style_conditional.spacer_height != "": 434 [hlines_$counter]
435 #if $track.track_file_style_conditional.title:
436 title = $track.track_file_style_conditional.title
437 #end if
438 #if $track.track_file_style_conditional.height:
439 height = $track.track_file_style_conditional.height
440 #end if
441 #if $track.track_file_style_conditional.min_value:
442 min_value = $track.track_file_style_conditional.min_value
443 #end if
444 #if $track.track_file_style_conditional.max_value:
445 max_value = $track.track_file_style_conditional.max_value
446 #end if
447 y_values = $track.track_file_style_conditional.y_values
448 show_data_range = $track.track_file_style_conditional.show_data
449 color = $track.track_file_style_conditional.color
450 alpha = $track.track_file_style_conditional.alpha
451 line_width = $track.track_file_style_conditional.line_width
452 line_style = $track.track_file_style_conditional.line_style
453 #if $track.track_file_style_conditional.invert_orientation:
454 orientation = inverted
455 #end if
456 overlay_previous = $track.track_file_style_conditional.overlay_select
457 file_type = hlines
458 ## If spacer is asked a new section is created:
459 #if $track.track_file_style_conditional.spacer_height != "":
442 [spacer] 460 [spacer]
443 height = $track.track_file_style_conditional.spacer_height 461 height = $track.track_file_style_conditional.spacer_height
444 #end if 462 #end if
445 #end if 463 #end if
464
465 ## Spacer
466 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
467 [spacer]
468 #if $track.track_file_style_conditional.spacer_height != "":
469 height = $track.track_file_style_conditional.spacer_height
470 #end if
471 #end if
446 #end for 472 #end for
447 473
448 #if $x_axis.x_axis_select == "yes": 474 #if $x_axis.x_axis_select == "true":
449 #if $x_axis.where == 'bottom': 475 #if $x_axis.where == 'bottom':
450 [x-axis] 476 [x-axis]
451 #if $x_axis.fontsize: 477 #if $x_axis.fontsize:
452 fontsize = $x_axis.fontsize 478 fontsize = $x_axis.fontsize
453 #end if 479 #end if
454 #if $x_axis.where: 480 where = bottom
455 where = $x_axis.where 481 #end if
456 #end if
457 #end if
458 #end if 482 #end if
459 </configfile> 483 </configfile>
460 </configfiles> 484 </configfiles>
461 <inputs> 485 <inputs>
462 <expand macro="region" /> 486 <expand macro="region" />
465 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph"> 489 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
466 <conditional name="track_file_style_conditional"> 490 <conditional name="track_file_style_conditional">
467 <param name="track_file_style_selector" type="select" label="Choose style of the track"> 491 <param name="track_file_style_selector" type="select" label="Choose style of the track">
468 <option value="hic_matrix_option">TAD visualization</option> 492 <option value="hic_matrix_option">TAD visualization</option>
469 <option value="chrom_states_option">Chromatine states</option> 493 <option value="chrom_states_option">Chromatine states</option>
470 <option value="tad_score_track_option">TAD score</option> 494 <option value="bedgraph_matrix_track_option">TAD score</option>
471 <option value="gene_track_option">Gene track / Bed track</option> 495 <option value="gene_track_option">Gene track / Bed track</option>
496 <option value="link_track_option">Link track</option>
472 <option value="narrow_peak_track_option">NarrowPeak track</option> 497 <option value="narrow_peak_track_option">NarrowPeak track</option>
473 <option value="bigwig_track_option">Bigwig track</option> 498 <option value="bigwig_track_option">Bigwig track</option>
474 <option value="bedgraph_track_option">Bedgraph track </option> 499 <option value="bedgraph_track_option">Bedgraph track </option>
475 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option> 500 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
476 <option value="vlines_track_option">Vlines track</option> 501 <option value="vlines_track_option">Vlines track</option>
502 <option value="hlines_track_option">Hlines track</option>
477 <option value="spacer_option">Spacer</option> 503 <option value="spacer_option">Spacer</option>
478 </param> 504 </param>
479 <when value="hic_matrix_option"> 505 <when value="hic_matrix_option">
480 <expand macro="plot_title" /> 506 <expand macro="plot_title" />
481 <expand macro="matrix_h5_cooler_multiple_macro" /> 507 <expand macro="matrix_h5_cooler_multiple_macro" />
485 <expand macro="minmax_macro" /> 511 <expand macro="minmax_macro" />
486 <param name="transform" type="select" label="Plot the transformed value"> 512 <param name="transform" type="select" label="Plot the transformed value">
487 <option value="log1p" selected="True" >log1p</option> 513 <option value="log1p" selected="True" >log1p</option>
488 <option value="log">log</option> 514 <option value="log">log</option>
489 <option value="-log">-log</option> 515 <option value="-log">-log</option>
490 <option value="">no transformation</option> 516 <option value="no">no transformation</option>
491 517
492 </param> 518 </param>
493 <param name="height_matrix" type="float" value="" optional="True" label="height"/> 519 <param name="height_matrix" type="float" value="" optional="True" label="height"/>
494 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" 520 <param name="show_masked_bins" type="boolean" truevalue="true" falsevalue="false" checked="false"
495 label="Show masked bins" /> 521 label="Show masked bins" />
496 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple='True'/> <!-- multiple='True'--> 522 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file" multiple="True"/>
497 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" /> 523 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
524 <param name="rasterize" type="boolean" truevalue="true" falsevalue="false" checked="true"
525 label="Rasterize the heatmap" />
498 <expand macro="inverted_macro" /> 526 <expand macro="inverted_macro" />
499 <expand macro="spacer_macro" />
500
501 </when>
502 <when value="tad_score_track_option">
503 <expand macro="plot_title" />
504 <expand macro="track_input_bedgraph_macro" />
505 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
506 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
507 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
508 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
509 <param name="height_tad" type="float" value="0.2" optional="True" label="height"/>
510 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" />
511 <expand macro="spacer_macro" /> 527 <expand macro="spacer_macro" />
512 528
513 </when> 529 </when>
514 <when value="chrom_states_option"> 530 <when value="chrom_states_option">
515 <expand macro="plot_title" /> 531 <expand macro="plot_title" />
516
517 <expand macro="track_input_bed_macro" /> 532 <expand macro="track_input_bed_macro" />
518 <expand macro="color_bed_macro" /> 533 <expand macro="color_bed_macro" />
534 <param name="line_width" type="float" value="0.5" label="width of lines" />
519 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/> 535 <param name="height_chrom" type="float" value="1.5" optional="True" label="height"/>
520 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" 536 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
521 label="Plot labels" /> 537 label="Plot labels" />
522 <expand macro="spacer_macro" /> 538 <expand macro="spacer_macro" />
523 539
524 </when> 540 </when>
525 <when value="gene_track_option"> 541 <when value="gene_track_option">
526 <expand macro="plot_title" /> 542 <expand macro="plot_title" />
527 543
528 <expand macro="track_input_bed_gtf_macro" /> 544 <expand macro="track_input_bed_gtf_macro" />
529 <expand macro="color_bed_macro" /> 545 <expand macro="color_bed_macro" />
530 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/> 546 <param name="height_bed" type="float" value="1.5" optional="True" label="height"/>
531 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" 547 <param name="labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
532 label="Plot labels" /> 548 label="Plot labels" />
533 <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/> 549 <param name="flybase" type="boolean" checked="true" label="Use flybase style" help="This will be only used for bed with 12 columns"/>
534 <param name="display" type="select" label="display to use"> 550 <param name="display" type="select" label="display to use">
535 <option value="stacked" selected="True">stacked (no overlap even with the label)</option> 551 <option value="stacked" selected="True">stacked (no overlap even with the label)</option>
536 <option value="interlaced">interlaced (everything on 2 lines)</option> 552 <option value="interleaved">interleaved (everything on 2 lines)</option>
537 <option value="collapsed">collapsed (everything on 1 line)</option> 553 <option value="collapsed">collapsed (everything on 1 line)</option>
538 <option value="domain">domain (only the first line of stacked)</option> 554 <option value="triangles">triangles (plot triangles between start and end)</option>
539 </param> 555 </param>
540 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false" 556 <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
541 label="Global max rows" /> 557 label="Include the arrowhead in the bed interval:"
542 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> 558 help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
543 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 559 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
560 <expand macro="bed_advanced_macro" />
561 <expand macro="overlay_macro" />
562 <expand macro="inverted_macro" />
544 <expand macro="spacer_macro" /> 563 <expand macro="spacer_macro" />
545 564
546 </when> 565 </when>
566 <when value="link_track_option">
567 <expand macro="plot_title" />
568 <expand macro="track_input_link_macro" />
569 <expand macro="links_color_macro" />
570 <expand macro="lines_macro" />
571 <param name="links_type" type="select" label="Representation of the link:">
572 <option value="arcs" selected="True">arcs (a line between the centers of the 2 regions)</option>
573 <option value="triangles">triangles</option>
574 <option value="loops">loops (a rectangle highlighting the intersection)</option>
575 </param>
576 <param name="height" type="float" value="1.5" optional="True" label="height"/>
577 <expand macro="minmax_macro" />
578 <expand macro="overlay_macro" />
579 <expand macro="inverted_macro" />
580 <expand macro="spacer_macro" />
581 </when>
547 <when value="narrow_peak_track_option"> 582 <when value="narrow_peak_track_option">
548 <expand macro="plot_title" /> 583 <expand macro="plot_title" />
549 <expand macro="track_input_narrow_peak_macro" /> 584 <expand macro="track_input_narrow_peak_macro" />
550 <param name="color" type="color" value="#000000" label="Color of track" optional="True" /> 585 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
551 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/> 586 <param name="height_narrow_peak" type="float" value="1.5" optional="True" label="height"/>
553 <param name="display_selector" type="select" label="display to use"> 588 <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> 589 <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> 590 <option value="box">box: Draw a box</option>
556 </param> 591 </param>
557 <when value="peak"> 592 <when value="peak">
558 <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true" 593 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
559 optional="True" label="Use summit information to make the curve." /> 594 optional="True" label="Use summit information to make the curve." />
560 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" 595 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false"
561 label="Show visualization of data range" /> 596 label="Show visualization of data range" />
562 <param name='width_adjust' type="float" value="1.5" optional="True" 597 <param name="width_adjust" type="float" value="1.5" optional="True"
563 label="Factor to change the width of the curve."/> 598 label="Factor to change the width of the curve."/>
564 <expand macro="minmax_macro" /> 599 <expand macro="minmax_macro" />
565 </when> 600 </when>
566 <when value="box"> 601 <when value="box">
567 <param name='use_summit' type="boolean" truevalue="yes" falsevalue="no" checked="true" 602 <param name="use_summit" type="boolean" truevalue="true" falsevalue="false" checked="true"
568 optional="True" label="Plot a vertical bar at the summit position." /> 603 optional="True" label="Plot a vertical bar at the summit position." />
569 </when> 604 </when>
570 </conditional> 605 </conditional>
571 <param name="show_labels" type="boolean" truevalue="yes" falsevalue="no" checked="true" 606 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="true"
572 label="Plot labels (name, p-val, q-val)" /> 607 label="Plot labels (name, p-val, q-val)" />
573 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 608 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
609 <expand macro="overlay_macro" />
610 <expand macro="inverted_macro" />
574 <expand macro="spacer_macro" /> 611 <expand macro="spacer_macro" />
575 612
576 </when> 613 </when>
577 <when value="bedgraph_track_option"> 614 <when value="bedgraph_track_option">
578 <expand macro="plot_title" /> 615 <expand macro="plot_title" />
579 <expand macro="track_input_bedgraph_macro" /> 616 <expand macro="track_input_bedgraph_macro" />
580 <expand macro="color_coverage_macro" /> 617 <expand macro="color_coverage_macro" />
581 <expand macro="minmax_macro" /> 618 <expand macro="minmax_macro" />
582 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> 619 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
583 <expand macro="type_coverage_macro" /> 620 <expand macro="type_coverage_macro" />
584 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range" /> 621 <param name="nans_to_zeros" type="boolean" truevalue="true" falsevalue="false" checked="false"
622 label="NAN's to zeros" />
623 <param name="use_middle" type="boolean" truevalue="true" falsevalue="false" checked="false"
624 label="Use middle: Instead of using start and end, use the middle of intervals (useful for 4C-seq tracks)." />
625 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" />
585 <expand macro="inverted_macro" /> 626 <expand macro="inverted_macro" />
586 <expand macro="overlay_macro" /> 627 <expand macro="overlay_macro" />
587 <expand macro="spacer_macro" /> 628 <expand macro="spacer_macro" />
588
589 </when> 629 </when>
590 <when value="bigwig_track_option"> 630 <when value="bigwig_track_option">
591 <expand macro="plot_title" /> 631 <expand macro="plot_title" />
592 632
593 <expand macro="track_input_bigwig_macro" /> 633 <expand macro="track_input_bigwig_macro" />
597 637
598 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/> 638 <param name="height_bigwig" type="float" value="1.5" optional="True" label="height"/>
599 <expand macro="reading_bw_macro" /> 639 <expand macro="reading_bw_macro" />
600 <expand macro="type_coverage_macro" /> 640 <expand macro="type_coverage_macro" />
601 <expand macro="type_coverage_macro" /> 641 <expand macro="type_coverage_macro" />
602 <param name="show_data" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Show visualization of data range"/> 642 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
603 <expand macro="inverted_macro" /> 643 <expand macro="inverted_macro" />
604 <expand macro="overlay_macro" /> 644 <expand macro="overlay_macro" />
605 <expand macro="spacer_macro" /> 645 <expand macro="spacer_macro" />
606 646
607 </when> 647 </when>
608 648
609
610 <when value="bedgraph_matrix_track_option"> 649 <when value="bedgraph_matrix_track_option">
611 <expand macro="plot_title" /> 650 <expand macro="plot_title" />
612 651
613 <expand macro="track_input_bedgraph_matrix_macro" /> 652 <expand macro="track_input_bedgraph_matrix_macro" />
614 <expand macro="minmax_macro" /> 653 <expand macro="minmax_macro" />
615 654
616 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/> 655 <param name="height_bedgraph" type="float" value="1.5" optional="True" label="height"/>
617 656
618 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false" 657 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
619 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead 658 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
620 of the matrix set to lines if a heatmap representing the matrix is not wanted"/> 659 of the matrix."/>
660 <param name="pos_score_in_bin" type="select" label="Position of the score with respect to bin start and end" help="Only used when type is lines">
661 <option value="center" selected="True">Center</option>
662 <option value="block">Block (draw a horizontal line between start and end)</option>
663 </param>
664 <param name="plot_horizontal_lines" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Plot an horizontal line at 0 when type is lines" />
665 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range" />
621 <expand macro="inverted_macro" /> 666 <expand macro="inverted_macro" />
622 <expand macro="spacer_macro" /> 667 <expand macro="spacer_macro" />
623 668
624 </when> 669 </when>
625 <when value="vlines_track_option"> 670 <when value="vlines_track_option">
626 <expand macro="track_input_bed_single_macro" /> 671 <expand macro="track_input_bed_single_macro" />
627 </when> 672 </when>
673 <when value="hlines_track_option">
674 <expand macro="plot_title" />
675 <param name="y_values" type="text" value="10, 200" label="Values where horizontal lines should be plotted separated by comma"/>
676 <param name="color" type="color" value="#000000" label="Color of line(s)" optional="True" />
677 <expand macro="lines_macro" />
678 <param name="height" type="float" value="1.5" optional="True" label="height"/>
679 <expand macro="minmax_macro" />
680 <param name="show_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show visualization of data range"/>
681 <expand macro="inverted_macro" />
682 <expand macro="overlay_macro" />
683 <expand macro="spacer_macro" />
684 </when>
628 <when value="spacer_option"> 685 <when value="spacer_option">
629 <expand macro="spacer_macro" /> 686 <param name="spacer_height" type="float" value="" optional="True"
687 label="Height of the spacer."/>
630 </when> 688 </when>
631 </conditional> 689 </conditional>
632 690
633 </repeat> 691 </repeat>
634 692
635 693
636 <conditional name="x_axis"> 694 <conditional name="x_axis">
637 <param name="x_axis_select" type="select" label="Configure x-axis"> 695 <param name="x_axis_select" type="select" label="Configure x-axis">
638 <option value="no" selected="True">No</option> 696 <option value="false" selected="True">No</option>
639 <option value="yes">Yes</option> 697 <option value="true">Yes</option>
640 </param> 698 </param>
641 <when value="yes"> 699 <when value="true">
642 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 700 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
643 <param name="where" type="select" label="Where to place the x-axis"> 701 <param name="where" type="select" label="Where to place the x-axis">
644 <option value="top" selected="True">Top</option> 702 <option value="top" selected="True">Top</option>
645 <option value="bottom">Bottom</option> 703 <option value="bottom">Bottom</option>
646 </param> 704 </param>
647 </when> 705 </when>
648 <when value="no" /> 706 <when value="false" />
649 </conditional> 707 </conditional>
650 <param name="image_file_format" type="select" label="Image output format"> 708 <param name="image_file_format" type="select" label="Image output format">
651 <option value="png">png</option> 709 <option value="png">png</option>
652 <option value="svg">svg</option> 710 <option value="svg">svg</option>
653 </param> 711 </param>
662 </outputs> 720 </outputs>
663 <tests> 721 <tests>
664 <test> 722 <test>
665 <param name="region" value="chrX:3000000-3500000"/> 723 <param name="region" value="chrX:3000000-3500000"/>
666 <conditional name="x_axis"> 724 <conditional name="x_axis">
667 <param name="x_axis_select" value="yes" /> 725 <param name="x_axis_select" value="true" />
668 </conditional> 726 </conditional>
669 <repeat name="tracks"> 727 <repeat name="tracks">
670 <conditional name="track_file_style_conditional"> 728 <conditional name="track_file_style_conditional">
671 <param name="track_file_style_selector" value="hic_matrix_option" /> 729 <param name="track_file_style_selector" value="hic_matrix_option" />
672 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 730 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
673 <param name="title" value="Kc DpnII (Li et al. 2015)" /> 731 <param name="title" value="Kc DpnII (Li et al. 2015)" />
674 <param name="colormap" value="RdYlBu_r" /> 732 <param name="colormap" value="RdYlBu_r" />
675 <param name="depth" value="200000" /> 733 <param name="depth" value="200000" />
676 <param name="transform" value="log1p" /> 734 <param name="transform" value="log1p" />
677 <param name="boundaries_file" value="domains.bed" /> 735 <param name="boundaries_file" value="domains.bed" />
678 <param name="x_labels" value="True" />
679 </conditional> 736 </conditional>
680 </repeat> 737 </repeat>
681 <repeat name="tracks"> 738 <repeat name="tracks">
682 <conditional name="track_file_style_conditional"> 739 <conditional name="track_file_style_conditional">
683 <param name="track_file_style_selector" value="spacer_option" /> 740 <param name="track_file_style_selector" value="spacer_option" />
688 <conditional name="track_file_style_conditional"> 745 <conditional name="track_file_style_conditional">
689 <param name="track_file_style_selector" value="chrom_states_option" /> 746 <param name="track_file_style_selector" value="chrom_states_option" />
690 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> 747 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
691 <param name="title" value="TAD state" /> 748 <param name="title" value="TAD state" />
692 <param name="height_chrom" value="0.5" /> 749 <param name="height_chrom" value="0.5" />
693 <param name="labels" value="off" /> 750 <param name="labels" value="false" />
694 <conditional name="color_bed"> 751 <conditional name="color_bed">
695 <param name="color_bed_select" value="bed_rgb" /> 752 <param name="color_bed_select" value="bed_rgb" />
696 </conditional> 753 </conditional>
697 </conditional> 754 </conditional>
698 </repeat> 755 </repeat>
699 <repeat name="tracks"> 756 <repeat name="tracks">
700 <conditional name="track_file_style_conditional"> 757 <conditional name="track_file_style_conditional">
701 <param name="track_file_style_selector" value="tad_score_track_option" /> 758 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
702 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" /> 759 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
703 <param name="title" value="TAD separation score (Ramirez et al.)" /> 760 <param name="title" value="TAD separation score (Ramirez et al.)" />
704 <param name="height_tad" value="10" /> 761 <param name="height_bedgraph" value="10" />
705 </conditional> 762 </conditional>
706 </repeat> 763 </repeat>
707 <repeat name="tracks"> 764 <repeat name="tracks">
708 <conditional name="track_file_style_conditional"> 765 <conditional name="track_file_style_conditional">
709 <param name="track_file_style_selector" value="spacer_option" /> 766 <param name="track_file_style_selector" value="spacer_option" />
798 <param name="track_file_style_selector" value="gene_track_option" /> 855 <param name="track_file_style_selector" value="gene_track_option" />
799 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" /> 856 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
800 <param name="title" value="max num rows 3" /> 857 <param name="title" value="max num rows 3" />
801 <param name="height_bed" value="3" /> 858 <param name="height_bed" value="3" />
802 <param name="fontsize" value="8" /> 859 <param name="fontsize" value="8" />
803 <param name="gene_rows" value="3" /> 860 <section name="bed_advanced">
861 <param name="gene_rows" value="3" />
862 </section>
804 </conditional> 863 </conditional>
805 </repeat> 864 </repeat>
806 <repeat name="tracks"> 865 <repeat name="tracks">
807 <conditional name="track_file_style_conditional"> 866 <conditional name="track_file_style_conditional">
808 <param name="track_file_style_selector" value="spacer_option" /> 867 <param name="track_file_style_selector" value="spacer_option" />
814 <param name="track_file_style_selector" value="gene_track_option" /> 873 <param name="track_file_style_selector" value="gene_track_option" />
815 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> 874 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
816 <param name="title" value="bed6 global max row" /> 875 <param name="title" value="bed6 global max row" />
817 <param name="height_bed" value="20" /> 876 <param name="height_bed" value="20" />
818 <param name="fontsize" value="10" /> 877 <param name="fontsize" value="10" />
819 <param name="global_max_row" value="True" /> 878 <section name="bed_advanced">
879 <param name="global_max_row" value="true" />
880 </section>
820 </conditional> 881 </conditional>
821 </repeat> 882 </repeat>
822 <repeat name="tracks"> 883 <repeat name="tracks">
823 <conditional name="track_file_style_conditional"> 884 <conditional name="track_file_style_conditional">
824 <param name="track_file_style_selector" value="vlines_track_option" /> 885 <param name="track_file_style_selector" value="vlines_track_option" />
825 <param name="track_input_bed_single" value="domains.bed" ftype="bed" /> 886 <param name="track_input_bed_single" value="domains.bed" ftype="bed" />
826 <param name="type" value="vlines" />
827 </conditional> 887 </conditional>
828 </repeat> 888 </repeat>
829 <param name="image_file_format" value="png" /> 889 <param name="image_file_format" value="png" />
830 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" /> 890 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
831 </test> 891 </test>
832 <test> 892 <test>
833 <param name="region" value="chrX:3000000-3500000"/> 893 <param name="region" value="chrX:3000000-3500000"/>
834 <conditional name="x_axis"> 894 <conditional name="x_axis">
835 <param name="x_axis_select" value="yes" /> 895 <param name="x_axis_select" value="true" />
836 </conditional> 896 </conditional>
837 <repeat name="tracks"> 897 <repeat name="tracks">
838 <conditional name="track_file_style_conditional"> 898 <conditional name="track_file_style_conditional">
839 <param name="track_file_style_selector" value="bigwig_track_option" /> 899 <param name="track_file_style_selector" value="bigwig_track_option" />
840 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" /> 900 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw,bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
845 <param name="type_selector" value="line_option" /> 905 <param name="type_selector" value="line_option" />
846 <param name="width_line" value="1" /> 906 <param name="width_line" value="1" />
847 </conditional> 907 </conditional>
848 </conditional> 908 </conditional>
849 </repeat> 909 </repeat>
910 <repeat name="tracks">
911 <conditional name="track_file_style_conditional">
912 <param name="track_file_style_selector" value="bigwig_track_option" />
913 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
914 <param name="title" value="nans_to_zeros" />
915 <param name="height_bigwig" value="4" />
916 <param name="color" value="blue" />
917 <section name="reading_bw_conditional">
918 <param name="nans_to_zeros" value="true" />
919 </section>
920 <param name="show_data" value="true" />
921 <conditional name="type_conditional">
922 <param name="type_selector" value="line_option" />
923 <param name="width_line" value="1" />
924 </conditional>
925 </conditional>
926 </repeat>
927 <repeat name="tracks">
928 <conditional name="track_file_style_conditional">
929 <param name="track_file_style_selector" value="hlines_track_option" />
930 <param name="title" value="" />
931 <param name="color" value="orange" />
932 <param name="y_values" value="50" />
933 <param name="line_width" value="2" />
934 <param name="line_style" value="dashed" />
935 <param name="overlay_select" value="share-y" />
936 </conditional>
937 </repeat>
938 <repeat name="tracks">
939 <conditional name="track_file_style_conditional">
940 <param name="track_file_style_selector" value="hlines_track_option" />
941 <param name="title" value="hlines" />
942 <param name="color" value="purple" />
943 <param name="y_values" value="0, 10, 20, 100" />
944 <param name="min_value" value="12" />
945 <param name="show_data" value="true" />
946 <param name="invert_orientation" value="true" />
947 </conditional>
948 </repeat>
850 <param name="image_file_format" value="png" /> 949 <param name="image_file_format" value="png" />
851 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" /> 950 <output name="outFileName" file="bigwig_multiple.png" ftype="png" compare="sim_size" delta="35000" />
852 </test> 951 </test>
853 <test> 952 <test>
854 <param name="region" value="chrX:3000000-3500000"/> 953 <param name="region" value="chrX:3000000-3500000"/>
855 <conditional name="x_axis"> 954 <conditional name="x_axis">
856 <param name="x_axis_select" value="yes" /> 955 <param name="x_axis_select" value="true" />
857 </conditional> 956 </conditional>
858 <repeat name="tracks"> 957 <repeat name="tracks">
859 <conditional name="track_file_style_conditional"> 958 <conditional name="track_file_style_conditional">
860 <param name="track_file_style_selector" value="hic_matrix_option" /> 959 <param name="track_file_style_selector" value="hic_matrix_option" />
861 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 960 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
870 <conditional name="track_file_style_conditional"> 969 <conditional name="track_file_style_conditional">
871 <param name="track_file_style_selector" value="chrom_states_option" /> 970 <param name="track_file_style_selector" value="chrom_states_option" />
872 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" /> 971 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
873 <param name="title" value="TAD state" /> 972 <param name="title" value="TAD state" />
874 <param name="height_chrom" value="0.5" /> 973 <param name="height_chrom" value="0.5" />
875 <param name="labels" value="off" /> 974 <param name="labels" value="false" />
876 <conditional name="color_bed"> 975 <conditional name="color_bed">
877 <param name="color_bed_select" value="bed_rgb" /> 976 <param name="color_bed_select" value="bed_rgb" />
878 </conditional> 977 </conditional>
879 </conditional> 978 </conditional>
880 </repeat> 979 </repeat>
883 <param name="track_file_style_selector" value="hic_matrix_option" /> 982 <param name="track_file_style_selector" value="hic_matrix_option" />
884 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/> 983 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
885 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" /> 984 <param name="title" value="Kc DpnII (Li et al. 2015) inverted no transform" />
886 <param name="colormap" value="Reds" /> 985 <param name="colormap" value="Reds" />
887 <param name="depth" value="200000" /> 986 <param name="depth" value="200000" />
888 <param name="transform" value="" /> 987 <param name="transform" value="no" />
889 <param name="invert_orientation" value="yes" /> 988 <param name="invert_orientation" value="true" />
890 <param name="min_value" value="5" /> 989 <param name="min_value" value="5" />
891 <param name="max_value" value="70" /> 990 <param name="max_value" value="70" />
892 </conditional> 991 </conditional>
893 </repeat> 992 </repeat>
894 <repeat name="tracks"> 993 <repeat name="tracks">
903 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" /> 1002 <param name="track_input_bedgraph" value="test_with_neg_values.bg.gz" ftype="bedgraph" />
904 <param name="title" value="bedgraph with negative values" /> 1003 <param name="title" value="bedgraph with negative values" />
905 <param name="height_bedgraph" value="4" /> 1004 <param name="height_bedgraph" value="4" />
906 <param name="color" value="black" /> 1005 <param name="color" value="black" />
907 <conditional name="color_negative"> 1006 <conditional name="color_negative">
908 <param name="color_negative_select" value="yes" /> 1007 <param name="color_negative_select" value="true" />
909 <param name="color" value="red" /> 1008 <param name="color" value="red" />
910 </conditional> 1009 </conditional>
911 <conditional name="type_conditional"> 1010 <conditional name="type_conditional">
912 <param name="type_selector" value="fill_option" /> 1011 <param name="type_selector" value="fill_option" />
913 </conditional> 1012 </conditional>
1001 <param name="track_file_style_selector" value="gene_track_option" /> 1100 <param name="track_file_style_selector" value="gene_track_option" />
1002 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" /> 1101 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
1003 <param name="title" value="bed6 global max row color from score" /> 1102 <param name="title" value="bed6 global max row color from score" />
1004 <param name="height_bed" value="20" /> 1103 <param name="height_bed" value="20" />
1005 <param name="fontsize" value="10" /> 1104 <param name="fontsize" value="10" />
1006 <param name="global_max_row" value="True" /> 1105 <section name="bed_advanced">
1106 <param name="global_max_row" value="true" />
1107 </section>
1007 <conditional name="color_bed"> 1108 <conditional name="color_bed">
1008 <param name="color_bed_select" value="colormap" /> 1109 <param name="color_bed_select" value="colormap" />
1009 <param name="color" value="RdYlBu_r" /> 1110 <param name="color" value="RdYlBu_r" />
1010 </conditional> 1111 </conditional>
1011 </conditional> 1112 </conditional>
1012 </repeat> 1113 </repeat>
1013 <repeat name="tracks"> 1114 <repeat name="tracks">
1014 <conditional name="track_file_style_conditional"> 1115 <conditional name="track_file_style_conditional">
1015 <param name="track_file_style_selector" value="gene_track_option" /> 1116 <param name="track_file_style_selector" value="gene_track_option" />
1016 <param name="track_input_bed" value="domains.bed" ftype="bed" /> 1117 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1017 <param name="title" value="domains.bed using the 9th field for colors interlaced" /> 1118 <param name="title" value="domains.bed using the 9th field for colors interleaved" />
1018 <param name="height_bed" value="2" /> 1119 <param name="height_bed" value="2" />
1019 <param name="fontsize" value="10" /> 1120 <param name="fontsize" value="10" />
1020 <conditional name="color_bed"> 1121 <conditional name="color_bed">
1021 <param name="color_bed_select" value="bed_rgb" /> 1122 <param name="color_bed_select" value="bed_rgb" />
1022 </conditional> 1123 </conditional>
1023 <param name="display" value="interlaced" /> 1124 <param name="border_color" value="red" />
1125 <param name="labels" value="false" />
1126 <param name="display" value="interleaved" />
1024 </conditional> 1127 </conditional>
1025 </repeat> 1128 </repeat>
1026 <param name="image_file_format" value="png" /> 1129 <param name="image_file_format" value="png" />
1027 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" /> 1130 <output name="outFileName" file="master_TADs_BW_plot.png" ftype="png" compare="sim_size" delta="35000" />
1028 </test> 1131 </test>
1029 <test> 1132 <test>
1030 <param name="region" value="X:2700000-3100000"/> 1133 <param name="region" value="X:2700000-3100000"/>
1031 <conditional name="x_axis"> 1134 <conditional name="x_axis">
1032 <param name="x_axis_select" value="yes" /> 1135 <param name="x_axis_select" value="true" />
1033 <param name="where" value="bottom" /> 1136 <param name="where" value="bottom" />
1034 </conditional> 1137 </conditional>
1035 <repeat name="tracks"> 1138 <repeat name="tracks">
1036 <conditional name="track_file_style_conditional"> 1139 <conditional name="track_file_style_conditional">
1037 <param name="track_file_style_selector" value="bigwig_track_option" /> 1140 <param name="track_file_style_selector" value="bigwig_track_option" />
1062 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" /> 1165 <output name="outFileName" file="test_alpha.png" ftype="png" compare="sim_size" delta="35000" />
1063 </test> 1166 </test>
1064 <test> 1167 <test>
1065 <param name="region" value="X:3000000-3300000"/> 1168 <param name="region" value="X:3000000-3300000"/>
1066 <conditional name="x_axis"> 1169 <conditional name="x_axis">
1067 <param name="x_axis_select" value="yes" /> 1170 <param name="x_axis_select" value="true" />
1068 </conditional> 1171 </conditional>
1069 <repeat name="tracks"> 1172 <repeat name="tracks">
1070 <conditional name="track_file_style_conditional"> 1173 <conditional name="track_file_style_conditional">
1071 <param name="track_file_style_selector" value="gene_track_option" /> 1174 <param name="track_file_style_selector" value="gene_track_option" />
1072 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" /> 1175 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1092 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" /> 1195 <output name="outFileName" file="test_gtf_bed4.png" ftype="png" compare="sim_size" delta="35000" />
1093 </test> 1196 </test>
1094 <test> 1197 <test>
1095 <param name="region" value="X:2760000-2802000"/> 1198 <param name="region" value="X:2760000-2802000"/>
1096 <conditional name="x_axis"> 1199 <conditional name="x_axis">
1097 <param name="x_axis_select" value="yes" /> 1200 <param name="x_axis_select" value="true" />
1098 <param name="where" value="bottom" /> 1201 <param name="where" value="bottom" />
1099 </conditional> 1202 </conditional>
1100 <repeat name="tracks"> 1203 <repeat name="tracks">
1101 <conditional name="track_file_style_conditional"> 1204 <conditional name="track_file_style_conditional">
1102 <param name="track_file_style_selector" value="narrow_peak_track_option" /> 1205 <param name="track_file_style_selector" value="narrow_peak_track_option" />
1104 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> 1207 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
1105 <param name="color" value="#9bbb59" /> 1208 <param name="color" value="#9bbb59" />
1106 <param name="height_narrow_peak" value="4" /> 1209 <param name="height_narrow_peak" value="4" />
1107 <conditional name="display"> 1210 <conditional name="display">
1108 <param name="display_selector" value="box" /> 1211 <param name="display_selector" value="box" />
1109 <param name="use_summit" value="yes" /> 1212 <param name="use_summit" value="true" />
1110 </conditional> 1213 </conditional>
1111 <param name="show_labels" value="yes" /> 1214 <param name="show_labels" value="true" />
1112 </conditional> 1215 </conditional>
1113 </repeat> 1216 </repeat>
1114 <repeat name="tracks"> 1217 <repeat name="tracks">
1115 <conditional name="track_file_style_conditional"> 1218 <conditional name="track_file_style_conditional">
1116 <param name="track_file_style_selector" value="narrow_peak_track_option" /> 1219 <param name="track_file_style_selector" value="narrow_peak_track_option" />
1118 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> 1221 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
1119 <param name="color" value="#c0504d" /> 1222 <param name="color" value="#c0504d" />
1120 <param name="height_narrow_peak" value="4" /> 1223 <param name="height_narrow_peak" value="4" />
1121 <conditional name="display"> 1224 <conditional name="display">
1122 <param name="display_selector" value="peak" /> 1225 <param name="display_selector" value="peak" />
1123 <param name="use_summit" value="yes" /> 1226 <param name="use_summit" value="true" />
1124 <param name="show_data" value="yes" /> 1227 <param name="show_data" value="true" />
1125 <param name="width_adjust" value="3" /> 1228 <param name="width_adjust" value="3" />
1126 <param name="max_value" value="50" /> 1229 <param name="max_value" value="50" />
1127 </conditional> 1230 </conditional>
1128 <param name="show_labels" value="no" /> 1231 <param name="show_labels" value="false" />
1129 <param name="spacer_height" value="0.5"/> 1232 <param name="spacer_height" value="0.5"/>
1130 </conditional> 1233 </conditional>
1131 </repeat> 1234 </repeat>
1132 <repeat name="tracks"> 1235 <repeat name="tracks">
1133 <conditional name="track_file_style_conditional"> 1236 <conditional name="track_file_style_conditional">
1136 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" /> 1239 <param name="track_input_narrow_peak" value="test2.narrowPeak" ftype="encodepeak" />
1137 <param name="color" value="#000000" /> 1240 <param name="color" value="#000000" />
1138 <param name="height_narrow_peak" value="4" /> 1241 <param name="height_narrow_peak" value="4" />
1139 <conditional name="display"> 1242 <conditional name="display">
1140 <param name="display_selector" value="peak" /> 1243 <param name="display_selector" value="peak" />
1141 <param name="use_summit" value="no" /> 1244 <param name="use_summit" value="false" />
1142 <param name="show_data" value="no" /> 1245 <param name="show_data" value="false" />
1143 </conditional> 1246 </conditional>
1144 <param name="show_labels" value="yes" /> 1247 <param name="show_labels" value="true" />
1145 </conditional> 1248 </conditional>
1146 </repeat> 1249 </repeat>
1147 <param name="image_file_format" value="png" /> 1250 <param name="image_file_format" value="png" />
1148 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" /> 1251 <output name="outFileName" file="test_narrowPeak.png" ftype="png" compare="sim_size" delta="35000" />
1252 </test>
1253 <test>
1254 <param name="region" value="chrX:3300000-3500000"/>
1255 <conditional name="x_axis">
1256 <param name="x_axis_select" value="true" />
1257 </conditional>
1258 <repeat name="tracks">
1259 <conditional name="track_file_style_conditional">
1260 <param name="track_file_style_selector" value="gene_track_option" />
1261 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1262 <param name="title" value="genes" />
1263 <param name="height_bed" value="10" />
1264 </conditional>
1265 </repeat>
1266 <repeat name="tracks">
1267 <conditional name="track_file_style_conditional">
1268 <param name="track_file_style_selector" value="gene_track_option" />
1269 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1270 <param name="title" value="gtf" />
1271 <param name="height_bed" value="10" />
1272 <section name="bed_advanced">
1273 <section name ="flybase">
1274 <param name="height_utr" value="0.75"/>
1275 <param name="color_utr" value="#ff0000"/>
1276 </section>
1277 <section name ="gtf">
1278 <param name="prefered_name" value="gene_name"/>
1279 <param name="merge_transcripts" value="true"/>
1280 </section>
1281 </section>
1282 </conditional>
1283 </repeat>
1284 <param name="image_file_format" value="png" />
1285 <output name="outFileName" file="test_gtf_flybase_param.png" ftype="png" compare="sim_size" delta="35000" />
1286 </test>
1287 <test>
1288 <param name="region" value="chrX:3300000-3500000"/>
1289 <conditional name="x_axis">
1290 <param name="x_axis_select" value="true" />
1291 </conditional>
1292 <repeat name="tracks">
1293 <conditional name="track_file_style_conditional">
1294 <param name="track_file_style_selector" value="gene_track_option" />
1295 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1296 <param name="title" value="dm3_genes.bed" />
1297 <param name="height_bed" value="10" />
1298 <param name="flybase" value="false" />
1299 <section name="bed_advanced">
1300 <param name="global_max_row" value="true" />
1301 <param name="max_labels" value="15" />
1302 </section>
1303 </conditional>
1304 </repeat>
1305 <repeat name="tracks">
1306 <conditional name="track_file_style_conditional">
1307 <param name="track_file_style_selector" value="gene_track_option" />
1308 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
1309 <param name="title" value="genes.bed.gz" />
1310 <param name="height_bed" value="10" />
1311 <param name="flybase" value="false" />
1312 <section name="bed_advanced">
1313 <param name="line_width" value="2"/>
1314 <section name ="ucsc">
1315 <param name="arrow_interval" value="10"/>
1316 </section>
1317 </section>
1318 </conditional>
1319 </repeat>
1320 <param name="image_file_format" value="png" />
1321 <output name="outFileName" file="test_ucsc_param.png" ftype="png" compare="sim_size" delta="35000" />
1322 </test>
1323 <test>
1324 <param name="region" value="X:3133000-3138000"/>
1325 <conditional name="x_axis">
1326 <param name="x_axis_select" value="true" />
1327 </conditional>
1328 <repeat name="tracks">
1329 <conditional name="track_file_style_conditional">
1330 <param name="track_file_style_selector" value="gene_track_option" />
1331 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1332 <param name="title" value="test" />
1333 <param name="height_bed" value="10" />
1334 <param name="flybase" value="true" />
1335 <param name="spacer_height" value="1"/>
1336 </conditional>
1337 </repeat>
1338 <repeat name="tracks">
1339 <conditional name="track_file_style_conditional">
1340 <param name="track_file_style_selector" value="gene_track_option" />
1341 <param name="track_input_bed" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
1342 <param name="title" value="test" />
1343 <param name="height_bed" value="10" />
1344 <conditional name="color_bed">
1345 <param name="color_bed_select" value="manually" />
1346 <param name="color" value="red" />
1347 </conditional>
1348 <param name="flybase" value="false" />
1349 <param name="spacer_height" value="1"/>
1350 </conditional>
1351 </repeat>
1352 <repeat name="tracks">
1353 <conditional name="track_file_style_conditional">
1354 <param name="track_file_style_selector" value="gene_track_option" />
1355 <param name="track_input_bed" value="dm3_subset_BDGP5.78.gtf.gz" ftype="gtf" />
1356 <param name="title" value="test" />
1357 <param name="height_bed" value="10" />
1358 <conditional name="color_bed">
1359 <param name="color_bed_select" value="manually" />
1360 <param name="color" value="red" />
1361 </conditional>
1362 <param name="flybase" value="true" />
1363 <param name="spacer_height" value="1"/>
1364 <param name="arrowhead_included" value="true"/>
1365 </conditional>
1366 </repeat>
1367 <repeat name="tracks">
1368 <conditional name="track_file_style_conditional">
1369 <param name="track_file_style_selector" value="vlines_track_option" />
1370 <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
1371 </conditional>
1372 </repeat>
1373 <param name="image_file_format" value="png" />
1374 <output name="outFileName" file="test_arrowhead_zoom.png" ftype="png" compare="sim_size" delta="35000" />
1375 </test>
1376 <test>
1377 <param name="region" value="X:3340000-3380000"/>
1378 <conditional name="x_axis">
1379 <param name="x_axis_select" value="true" />
1380 </conditional>
1381 <repeat name="tracks">
1382 <conditional name="track_file_style_conditional">
1383 <param name="track_file_style_selector" value="gene_track_option" />
1384 <param name="track_input_bed" value="domains.bed" ftype="bed" />
1385 <param name="height_bed" value="6" />
1386 <conditional name="color_bed">
1387 <param name="color_bed_select" value="manually" />
1388 <param name="color" value="yellow" />
1389 </conditional>
1390 <param name="display" value="triangles" />
1391 <param name="spacer_height" value="1"/>
1392 </conditional>
1393 </repeat>
1394 <repeat name="tracks">
1395 <conditional name="track_file_style_conditional">
1396 <param name="track_file_style_selector" value="bedgraph_track_option" />
1397 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
1398 <param name="title" value="bedgraph" />
1399 <param name="height_bedgraph" value="4" />
1400 <param name="color" value="blue" />
1401 <conditional name="type_conditional">
1402 <param name="type_selector" value="line_option" />
1403 </conditional>
1404 </conditional>
1405 </repeat>
1406 <repeat name="tracks">
1407 <conditional name="track_file_style_conditional">
1408 <param name="track_file_style_selector" value="bedgraph_track_option" />
1409 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
1410 <param name="title" value="bedgraph" />
1411 <param name="height_bedgraph" value="4" />
1412 <param name="color" value="blue" />
1413 <param name="use_middle" value="true" />
1414 <conditional name="type_conditional">
1415 <param name="type_selector" value="line_option" />
1416 </conditional>
1417 </conditional>
1418 </repeat>
1419 <param name="image_file_format" value="png" />
1420 <output name="outFileName" file="test_middle_triangle.png" ftype="png" compare="sim_size" delta="35000" />
1421 </test>
1422 <test>
1423 <param name="region" value="chrX:3250000-3400000"/>
1424 <conditional name="x_axis">
1425 <param name="x_axis_select" value="true" />
1426 </conditional>
1427 <repeat name="tracks">
1428 <conditional name="track_file_style_conditional">
1429 <param name="track_file_style_selector" value="hic_matrix_option" />
1430 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
1431 <param name="title" value="Kc DpnII (Li et al. 2015)" />
1432 <param name="colormap" value="RdYlBu_r" />
1433 <param name="depth" value="100000" />
1434 <param name="transform" value="log1p" />
1435 <param name="show_masked_bins" value="true" />
1436 <param name="scale_factor" value="2.0" />
1437 </conditional>
1438 </repeat>
1439 <repeat name="tracks">
1440 <conditional name="track_file_style_conditional">
1441 <param name="track_file_style_selector" value="spacer_option" />
1442 <param name="spacer_height" value="0.05" />
1443 </conditional>
1444 </repeat>
1445 <repeat name="tracks">
1446 <conditional name="track_file_style_conditional">
1447 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
1448 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
1449 <param name="title" value="TAD separation score (Ramirez et al.)" />
1450 <param name="height_bedgraph" value="10" />
1451 <param name="type_lines" value="lines" />
1452 <param name="pos_score_in_bin" value="block" />
1453 <param name="plot_horizontal_lines" value="true" />
1454 <param name="show_data" value="true" />
1455 </conditional>
1456 </repeat>
1457 <repeat name="tracks">
1458 <conditional name="track_file_style_conditional">
1459 <param name="track_file_style_selector" value="bedgraph_matrix_track_option" />
1460 <param name="track_input_bedgraph_matrix" value="tad_score.gz" ftype="bedgraph" />
1461 <param name="title" value="TAD separation score (Ramirez et al.)" />
1462 <param name="height_bedgraph" value="10" />
1463 <param name="type_lines" value="lines" />
1464 <param name="pos_score_in_bin" value="center" />
1465 <param name="plot_horizontal_lines" value="false" />
1466 </conditional>
1467 </repeat>
1468 <param name="image_file_format" value="png" />
1469 <output name="outFileName" file="test_TADs_bdgm.png" ftype="png" compare="sim_size" delta="35000" />
1470 </test>
1471 <test>
1472 <param name="region" value="chrX:3000000-3300000"/>
1473 <conditional name="x_axis">
1474 <param name="x_axis_select" value="true" />
1475 </conditional>
1476 <repeat name="tracks">
1477 <conditional name="track_file_style_conditional">
1478 <param name="track_file_style_selector" value="hic_matrix_option" />
1479 <param name="matrix_h5_cooler_multiple" value="Li_et_al_2015.h5"/>
1480 <param name="title" value="Kc DpnII (Li et al. 2015)" />
1481 <param name="colormap" value="Purples" />
1482 <param name="depth" value="190000" />
1483 <param name="transform" value="no" />
1484 </conditional>
1485 </repeat>
1486 <repeat name="tracks">
1487 <conditional name="track_file_style_conditional">
1488 <param name="track_file_style_selector" value="link_track_option" />
1489 <param name="track_input_link" value="test.arcs" ftype="bed" />
1490 <param name="title" value="" />
1491 <param name="line_width" value="10" />
1492 <param name="links_type" value="loops" />
1493 <conditional name="color_link">
1494 <param name="color_link_select" value="manually" />
1495 <param name="color" value="red" />
1496 </conditional>
1497 <param name="overlay_select" value="share-y" />
1498 </conditional>
1499 </repeat>
1500 <repeat name="tracks">
1501 <conditional name="track_file_style_conditional">
1502 <param name="track_file_style_selector" value="link_track_option" />
1503 <param name="track_input_link" value="test.arcs" ftype="bed" />
1504 <param name="title" value="" />
1505 <param name="height" value="5" />
1506 <conditional name="color_link">
1507 <param name="color_link_select" value="colormap" />
1508 <param name="color" value="hot" />
1509 </conditional>
1510 <param name="max_value" value="5"/>
1511 <param name="invert_orientation" value="true" />
1512 </conditional>
1513 </repeat>
1514 <param name="image_file_format" value="png" />
1515 <output name="outFileName" file="test_link.png" ftype="png" compare="sim_size" delta="35000" />
1149 </test> 1516 </test>
1150 </tests> 1517 </tests>
1151 <help><![CDATA[ 1518 <help><![CDATA[
1152 1519
1153 pyGenomeTracks 1520 pyGenomeTracks