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comparison hicPlotTADs.xml @ 2:f23f7178fae6 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
author bgruening
date Thu, 02 Nov 2017 11:12:48 -0400
parents 3615a7c5c119
children 50502e2beaaa
comparison
equal deleted inserted replaced
1:3615a7c5c119 2:f23f7178fae6
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicPlotTADs</token> 4 <token name="@BINARY@">hicPlotTADs</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="aggressive"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 sed '/^$/d' '$tracks_config' && 10 sed '/^$/d' '$tracks_config' &&
11
12 @BINARY@ 11 @BINARY@
13 --tracks '$tracks_config' 12 --tracks '$tracks_config'
14 #if $region and $region is not None: 13 #if $region and $region is not None:
15 --region '$region' 14 --region '$region'
16 #end if 15 #end if
17 --outFileName plot.svg 16 --outFileName plot.$image_file_format
18 17 && mv plot.$image_file_format plot
19 ]]> 18 ]]>
20 </command> 19 </command>
21 <configfiles> 20 <configfiles>
22 <configfile name="tracks_config"> 21 <configfile name="tracks_config">
23 ## lines that start with '#' are comment lines
24 ## and are not interpreted by the program
25 ## the different tracks are represented by sections in this file
26 ## each section starts with a header of the form [hic]
27 ## the content of the section label (in the previous example 'hic') is irrelevant for
28 ## plotting and only used to tell the user when something goes wrong.
29 ## There are two exceptions for this, the [x-axis] and the [spacer] sections
30 ## that use the secion label to determine the action.
31
32 #if $x_axis.x_axis_select == "yes": 22 #if $x_axis.x_axis_select == "yes":
33 [x-axis] 23 [x-axis]
34 #if $x_axis.fontsize: 24 #if $x_axis.fontsize:
35 fontsize = $x_axis.fontsize 25 fontsize = $x_axis.fontsize
36 #end if 26 #end if
37 #if $x_axis.where: 27 #if $x_axis.where:
38 where = $x_axis.where 28 where = $x_axis.where
39 #end if 29 #end if
40 #else: 30 #end if
41 [x-axis]
42 #end if
43
44 #for $counter, $track in enumerate($tracks): 31 #for $counter, $track in enumerate($tracks):
32 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
45 [hic_section_$counter] 33 [hic_section_$counter]
46 34 file = $track.track_file_style_conditional.track_input_h5
47 file = $track.track_input 35 file_type = hic_matrix
48 36 title = $track.track_file_style_conditional.title
49 #if $track.title 37 #if $track.track_file_style_conditional.depth:
50 title = $track.title 38 depth = $track.track_file_style_conditional.depth
51 #end if 39 #end if
52 40 #if $track.track_file_style_conditional.colormap:
53 #if $track.colormap and $track.track_input.ext == "h5": 41 colormap = $track.track_file_style_conditional.colormap
54 colormap = $track.colormap 42 #end if
55 #end if 43 #if $track.track_file_style_conditional.min_value:
56 44 min_value = $track.track_file_style_conditional.min_value
57 #if $track.color and $track.track_input.ext != "h5": 45 #end if
58 color = $track.color 46 #if $track.track_file_style_conditional.max_value:
59 #end if 47 max_value = $track.track_file_style_conditional.max_value
60 48 #end if
61 #if $track.border_color: 49 transform = $track.track_file_style_conditional.transform
62 color = $track.border_color 50 #if $track.track_file_style_conditional.boundaries_file:
63 #end if 51 boundaries_file = $track.track_file_style_conditional.boundaries_file
64 52 #end if
65 #if $track.depth: 53 #if $track.track_file_style_conditional.x_labels:
66 depth = $track.depth 54 x labels = $track.track_file_style_conditional.x_labels
67 #end if 55 #end if
68 56 #if $track.track_file_style_conditional.type:
69 #if $track.display: 57 type = $track.track_file_style_conditional.type
70 display = $track.display 58 #end if
71 #end if 59 #if $track.track_file_style_conditional.show_masked_bins:
72 60 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
73 #if $track.width 61 #end if
74 width = $track.width 62 #if $track.track_file_style_conditional.scale_factor:
75 #end if 63 scale factor = $track.track_file_style_conditional.scale_factor
76 64 #end if
77 #if $track.min_value: 65
78 # auto is possible 66 #end if
79 min_value = $track.min_value 67 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
80 #end if 68
81 69 [tad_score_$counter]
82 #if $track.max_value: 70 file = $track.track_file_style_conditional.track_input_bedgraph
83 max_value = $track.max_value 71 title = $track.track_file_style_conditional.title
84 #end if 72 #if $track.track_file_style_conditional.color:
85 73 color = $track.track_file_style_conditional.color
86 #if $track.transform 74 #end if
87 transform = $track.transform 75 #if $track.track_file_style_conditional.width_tad:
88 #end if 76 width = $track.track_file_style_conditional.width_tad
89 77 #end if
90 #if $track.boundaries_file: 78 #if $track.track_file_style_conditional.show_data:
91 boundaries_file = $track.boundaries_file 79 show data range = $track.track_file_style_conditional.show_data
92 #end if 80 #end if
93 81
94 #if $track.x_labels == 'yes': 82 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
95 x labels = yes
96 #end if
97
98 #if $track.track_input.ext == "bedgraph":
99 #set $columns = len(open(str($track.track_input)).readline().split('\t'))
100 #if $columns > 5: 83 #if $columns > 5:
101 file_type = bedgraph_matrix 84 file_type = bedgraph_matrix
102 #else: 85 #else:
103 file_type = bedgraph 86 file_type = bedgraph
104 #end if 87 #end if
105 #elif $track.track_input.ext == "h5": 88 type = lines
106 file_type = hic_matrix 89 #end if
107 #else 90 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
108 file_type = $track.track_input.ext 91
109 #end if 92 [chrom states_$counter]
110 93 file = $track.track_file_style_conditional.track_input_bed
111 ## show masked bins plots as white lines 94 title = $track.track_file_style_conditional.title
112 ## those bins that were not used during the correction 95 #if $track.track_file_style_conditional.color:
113 ## the default is to extend neighboring bins to 96 color = $track.track_file_style_conditional.color
114 ## obtain an aesthetically pleasant output 97 #end if
115 #if $track.show_masked_bins: 98 display = collapsed
116 show_masked_bins = $track.show_masked_bins 99 #if $track.track_file_style_conditional.width_chrom:
117 #end if 100 width = $track.track_file_style_conditional.width_chrom
118 101 #end if
119 #if $track.show_data_range: 102 #if $track.track_file_style_conditional.border_color:
120 show data range = $track.show_data_range 103 border_color = $track.track_file_style_conditional.border_color
121 #end if 104 #end if
122 105 file_type = bed
123 #if $track.nans_to_zeros: 106 #end if
124 nans to zeros = $track.nans_to_zeros 107 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
125 #end if 108
126 109 [genes_$counter]
127 ## to turn off/on printing of labels 110 file = $track.track_file_style_conditional.track_input_bed
128 #if str($track.labels) == 'off' 111 title = $track.track_file_style_conditional.title
129 labels = off 112 #if $track.track_file_style_conditional.color:
130 #end if 113 color = $track.track_file_style_conditional.color
131 114 #end if
132 #if $track.global_max_row == 'yes': 115
133 global max row = yes 116 #if $track.track_file_style_conditional.width_bed:
134 #end if 117 width = $track.track_file_style_conditional.width_bed
135 118 #end if
136 ## optional: font size can be given if default are not good 119
137 #if $track.fontsize: 120 #if $track.track_file_style_conditional.labels:
138 fontsize = $track.fontsize 121 labels = $track.track_file_style_conditional.labels
139 #end if 122 #end if
140 123
141 #if $track.number_of_bins: 124 #if $track.track_file_style_conditional.type:
142 number of bins = $track.number_of_bins 125 type = $track.track_file_style_conditional.type
143 #end if 126 #end if
144 127
145 #if $track.orientation 128 file_type = bed
146 orientation = $track.orientation 129 #if $track.track_file_style_conditional.fontsize:
147 #end if 130 fontsize = $track.track_file_style_conditional.fontsize
148 131 #end if
149 #if $track.type 132
150 type = $track.type 133 #if $track.track_file_style_conditional.gene_rows:
151 #end if 134 gene rows = $track.track_file_style_conditional.gene_rows
152 135 #end if
153 #if $track.gene_rows 136
154 gene rows = $track.gene_rows 137 #if $track.track_file_style_conditional.global_max_row:
155 #end if 138 global max row = $track.track_file_style_conditional.global_max_row
156 139 #end if
157 #if $track.spacer_width: 140
141 #end if
142
143
144 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
145
146 [bedgraph_$counter]
147 file = $track.track_file_style_conditional.track_input_bedgraph
148 title = $track.track_file_style_conditional.title
149 #if $track.track_file_style_conditional.color:
150 color = $track.track_file_style_conditional.color
151 #end if
152 #if $track.track_file_style_conditional.width_bedgraph:
153 width = $track.track_file_style_conditional.width_bedgraph
154 #end if
155 #if $track.track_file_style_conditional.show_data:
156 show data range = $track.track_file_style_conditional.show_data
157 #end if
158
159 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
160 #if $columns > 5:
161 file_type = bedgraph_matrix
162 #else:
163 file_type = bedgraph
164 #end if
165 type = lines
166 #end if
167
168 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
169
170 [bigwig_$counter]
171 file = $track.track_file_style_conditional.track_input_bigwig
172 title = $track.track_file_style_conditional.title
173 color = $track.track_file_style_conditional.color
174 #if $track.track_file_style_conditional.min_value:
175 min_value = $track.track_file_style_conditional.min_value
176 #else:
177 min_value = 0
178 #end if
179 #if $track.track_file_style_conditional.max_value:
180 max_value = $track.track_file_style_conditional.max_value
181 #else:
182 max_value = auto
183 #end if
184 width = $track.track_file_style_conditional.width_bigwig
185 #if $track.track_file_style_conditional.number_of_bins:
186 number of bins = $track.track_file_style_conditional.number_of_bins
187 #end if
188 nans to zeros = $track.track_file_style_conditional.nans_to_zeros
189 #if $track.track_file_style_conditional.type_conditional == 'fill_option':
190 type = fill
191 #elif $track.track_file_style_conditional.type_conditional == 'line_option':
192 type = line:$track.track_file_style_conditional.type_conditional.width_line
193 #elif $track.track_file_style_conditional.type_conditional == 'point_option':
194 type = points:$track.track_file_style_conditional.type_conditional.width_point
195 #end if
196 #if $track.track_file_style_conditional.data_range:
197 show data range = $track.track_file_style_conditional.data_range
198 #end if
199 file_type = bigwig
200 #end if
201 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
202
203 [bedgraph_matrix_$counter]
204 file = $track.track_file_style_conditional.track_input_bedgraph_matrix
205 title = $track.track_file_style_conditional.title
206 #if $track.track_file_style_conditional.width_bedgraph:
207 width = $track.track_file_style_conditional.width_bedgraph
208 #end if
209 orientation = inverted
210 #if $track.track_file_style_conditional.min_value:
211 min_value = $track.track_file_style_conditional.min_value
212 #end if
213 #if $track.track_file_style_conditional.max_value:
214 max_value = $track.track_file_style_conditional.max_value
215 #end if
216 #if $track.track_file_style_conditional.type_lines:
217 type = $track.track_file_style_conditional.type_lines
218 #end if
219 file_type = bedgraph_matrix
220 plot horizontal lines=False
221 #end if
222 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
223
224 [vlines_$counter]
225 file = $track.track_file_style_conditional.track_input_bed
226 type = vlines
227 file_type = bed
228 #end if
229 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
230
158 [spacer] 231 [spacer]
159 width = $track.spacer_width 232 #if $track.track_file_style_conditional.spacer_width:
160 #end if 233 width = $track.track_file_style_conditional.spacer_width
161 234 #end if
162 235 #end if
163 #end for</configfile> 236 #end for</configfile>
164 </configfiles> 237 </configfiles>
165 <inputs> 238 <inputs>
166 <expand macro="region" /> 239 <expand macro="region" />
240
167 <repeat name="tracks" min="1" title="Include tracks in your plot" 241 <repeat name="tracks" min="1" title="Include tracks in your plot"
168 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph"> 242 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
169 243 <conditional name="track_file_style_conditional">
170 <param name="track_input" type="data" format="h5,bed,bedgraph,bigwig,tabular" label="Track file"/> 244 <param name="track_file_style_selector" type="select" label="Choose style of the track">
171 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file"/> 245 <option value="hic_matrix_option">TAD visualization</option>
172 <param name="title" type="text" optional="true" label="Plot title"/> 246 <option value="chrom_states_option">Chromatine states</option>
173 <expand macro="colormap" /> 247 <option value="tad_score_track_option">TAD score</option>
174 <param name="color" type="color" value="#000000" label="Track color" optional="True" /> 248 <option value="gene_track_option">Gene track</option>
175 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" /> 249 <option value="bigwig_track_option">Bigwig track</option>
176 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/> 250 <option value="bedgraph_track_option">Bedgraph track </option>
177 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/> 251 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
178 252 <option value="vlines_track_option">Vlines track</option>
179 <param name="width" type="float" value="1.5" optional="True" label="Width"/> 253 <option value="spacer_option">Spacer</option>
180 254 </param>
181 <param name="transform" type="select" optional="True" label="Plot the transformed value"> 255 <when value="hic_matrix_option">
182 <option value="log1p">log1p</option> 256 <expand macro="plot_title" />
183 <option value="log">log</option> 257 <expand macro="track_input_h5_macro" />
184 </param> 258
185 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false" 259 <expand macro="colormap" />
186 label="Show masked bins" /> 260 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
187 261 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
188 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false" 262 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
189 label="NAN's to zeros" /> 263 <param name="transform" type="select" label="Plot the transformed value">
190 264 <option value="log1p" selected="True" >log1p</option>
191 <param name="show_data_range" type="boolean" truevalue="yes" falsevalue="no" checked="false" 265 <option value="log">log</option>
192 label="SHow data range" /> 266 <option value="-log">-log</option>
193 267
194 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true" 268 </param>
195 label="Plot labels" /> 269 <param name="type" type="select" optional="True" label="Plotting type">
196 270 <option value="arcplot">arcplot</option>
197 <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" checked="false" 271 <option value="interaction">interaction</option>
198 label="X labels" /> 272 </param>
199 273 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
200 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false" 274 label="Show masked bins" />
201 label="Global max rows" /> 275 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file"/>
202 276 <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" />
203 <param name="orientation" type="select" optional="True" label="Orientation"> 277 <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" />
204 <option value="inverted">Inverted</option> 278
205 </param> 279 </when>
206 280 <when value="tad_score_track_option">
207 <param name="display" type="select" optional="True" label="Display type"> 281 <expand macro="plot_title" />
208 <option value="collapsed">collapsed</option> 282 <expand macro="track_input_bedgraph_macro" />
209 <option value="domain">domain</option> 283 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
210 <option value="interlaced">interlaced</option> 284
211 </param> 285 <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/>
212 286 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
213 <param name="type" type="select" optional="True" label="Plotting type"> 287 </when>
214 <option value="lines">Lines</option> 288 <when value="chrom_states_option">
215 <option value="line">Line</option> 289 <expand macro="plot_title" />
216 <option value="vlines">vertical dotted lines from the top to the bottom</option> 290
217 <option value="arcplot">arcplot</option> 291 <expand macro="track_input_bed_macro" />
218 <option value="interaction">interaction</option> 292 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
219 <option value="genes">Genes</option> 293
220 </param> 294 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
221 295 <param name="width_chrom" type="float" value="1.5" optional="True" label="Width"/>
222 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" /> 296 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
223 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" /> 297 label="Plot labels" />
224 298 </when>
225 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" /> 299 <when value="gene_track_option">
226 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" /> 300 <expand macro="plot_title" />
227 301
228 <param name="spacer_width" type="float" value="" optional="True" 302 <expand macro="track_input_bed_macro" />
229 label="Include spacer at the end of the track." help="Width of the spacer." /> 303 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
230 304 <param name="width_bed" type="float" value="1.5" optional="True" label="Width"/>
305 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
306 label="Plot labels" />
307 <param name="type" type="select" optional="True" label="Type">
308 <option value="genes">genes</option>
309 <option value="domains">domains</option>
310 </param>
311 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
312 label="Global max rows" />
313 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
314 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
315
316 </when>
317 <when value="bedgraph_track_option">
318 <expand macro="plot_title" />
319 <expand macro="track_input_bedgraph_macro" />
320 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
321
322 <param name="width_bedgraph" type="float" value="0.2" optional="True" label="Width"/>
323 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
324 </when>
325 <when value="bigwig_track_option">
326 <expand macro="plot_title" />
327
328 <expand macro="track_input_bigwig_macro" />
329 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
330
331 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
332 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
333
334 <param name="width_bigwig" type="float" value="1.5" optional="True" label="Width"/>
335 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
336 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
337 label="NAN's to zeros" />
338 <conditional name="type_conditional">
339 <param name="type_selector" type="select" label="Choose style of the plot.">
340 <option value="fill_option">fill</option>
341 <option value="line_option">line</option>
342 <option value="point_option">point</option>
343 </param>
344 <when value="line_option">
345 <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
346 </when>
347 <when value="point_option">
348 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
349 </when>
350 <when value="fill_option" />
351 </conditional>
352 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
353 </when>
354
355
356 <when value="bedgraph_matrix_track_option">
357 <expand macro="plot_title" />
358
359 <expand macro="track_input_bedgraph_matrix_macro" />
360 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
361 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
362
363 <param name="width_bedgraph" type="float" value="1.5" optional="True" label="Width"/>
364
365 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
366 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
367 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
368 </when>
369 <when value="vlines_track_option">
370 <expand macro="track_input_bed_macro" />
371 </when>
372 <when value="spacer_option">
373 <expand macro="spacer_macro" />
374 </when>
375 </conditional>
376
231 </repeat> 377 </repeat>
232 378
379
233 <conditional name="x_axis"> 380 <conditional name="x_axis">
234 <param name="x_axis_select" type="select" label="Configure x-axis"> 381 <param name="x_axis_select" type="select" label="Configure x-axis">
235 <option value="no" selected="True">No</option> 382 <option value="no" selected="True">No</option>
236 <option value="yes">Yes</option> 383 <option value="yes">Yes</option>
237 </param> 384 </param>
242 <option value="bottom">Bottom</option> 389 <option value="bottom">Bottom</option>
243 </param> 390 </param>
244 </when> 391 </when>
245 <when value="no" /> 392 <when value="no" />
246 </conditional> 393 </conditional>
247 394 <param name="image_file_format" type="select" label="Image output format">
395 <option value="png">png</option>
396 <option value="svg">svg</option>
397 </param>
248 </inputs> 398 </inputs>
249 <outputs> 399 <outputs>
250 <data name="outFileName" from_work_dir="plot.svg" format="svg"/> 400 <data format="png" name="outFileName" from_work_dir="plot">
401 <change_format>
402 <when input="image_file_format" value="png" format="png" />
403 <when input="image_file_format" value="svg" format="svg" />
404 </change_format>
405 </data>
251 </outputs> 406 </outputs>
252 <tests> 407 <tests>
253 <test> 408 <test>
254 <param name="region" value="chrX:3000000-3500000"/> 409 <param name="region" value="chrX:3000000-3500000"/>
255 <repeat name="tracks"> 410 <conditional name="x_axis">
256 <param name="track_input" value="Li_et_al_2015.h5" ftype="h5" /> 411 <param name="x_axis_select" value="yes" />
257 <param name="title" value="Kc DpnII (Li et al. 2015)"/> 412 </conditional>
258 <param name="colormap" value="RdYlBu_r"/> 413 <repeat name="tracks">
259 <param name="depth" value="200000"/> 414 <conditional name="track_file_style_conditional">
260 <param name="transform" value="log1p"/> 415 <param name="track_file_style_selector" value="hic_matrix_option" />
261 <param name="boundaries_file" value="domains.bed"/> 416 <param name="track_input_h5" value="Li_et_al_2015.h5" ftype="h5" />
262 <param name="spacer_width" value="0.5"/> 417 <param name="title" value="Kc DpnII (Li et al. 2015)" />
263 </repeat> 418 <param name="colormap" value="RdYlBu_r" />
264 <repeat name="tracks"> 419 <param name="depth" value="200000" />
265 <param name="track_input" value="tad_classification.bed" ftype="bed" /> 420 <param name="transform" value="log1p" />
266 <param name="title" value="TAD state"/> 421 <param name="boundaries_file" value="domains.bed" />
267 <param name="width" value="0.5"/> 422 <param name="x_labels" value="True" />
268 <param name="display" value="collapsed"/> 423 </conditional>
269 <param name="labels" value="off"/> 424 </repeat>
270 </repeat> 425 <repeat name="tracks">
271 <repeat name="tracks"> 426 <conditional name="track_file_style_conditional">
272 <param name="track_input" value="tad_score.gz" ftype="bedgraph" /> 427 <param name="track_file_style_selector" value="spacer_option" />
273 <param name="title" value="TAD separation score (Ramirez et al.)"/> 428 <param name="spacer_width" value="0.05" />
274 <param name="width" value="10"/> 429 </conditional>
275 <param name="type" value="lines"/> 430 </repeat>
276 <param name="spacer_width" value="1"/> 431 <repeat name="tracks">
277 </repeat> 432 <conditional name="track_file_style_conditional">
278 <repeat name="tracks"> 433 <param name="track_file_style_selector" value="chrom_states_option" />
279 <param name="track_input" value="dm3_genes.bed.gz" ftype="bed" /> 434 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
280 <param name="title" value="genes"/> 435 <param name="title" value="TAD state" />
281 <param name="width" value="5"/> 436 <param name="width_chrom" value="0.5" />
282 <param name="fontsize" value="10"/> 437 <param name="labels" value="off" />
283 <param name="spacer_width" value="1"/> 438 </conditional>
284 </repeat> 439 </repeat>
285 <repeat name="tracks"> 440 <repeat name="tracks">
286 <param name="track_input" value="dm3_genes.bed.gz" ftype="bed" /> 441 <conditional name="track_file_style_conditional">
287 <param name="title" value="max num rows 3"/> 442 <param name="track_file_style_selector" value="tad_score_track_option" />
288 <param name="width" value="3"/> 443 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" />
289 <param name="fontsize" value="8"/> 444 <param name="title" value="TAD separation score (Ramirez et al.)" />
290 <param name="gene_rows" value="3"/> 445 <param name="width_tad" value="10" />
291 <param name="spacer_width" value="1"/> 446 </conditional>
292 </repeat> 447 </repeat>
293 <repeat name="tracks"> 448 <repeat name="tracks">
294 <param name="track_input" value="dm3_genes.bed6.gz" ftype="bed" /> 449 <conditional name="track_file_style_conditional">
295 <param name="title" value="bed6 global max row"/> 450 <param name="track_file_style_selector" value="spacer_option" />
296 <param name="width" value="20"/> 451 <param name="spacer_width" value="1" />
297 <param name="fontsize" value="10"/> 452 </conditional>
298 <param name="global_max_row" value="True"/> 453 </repeat>
299 </repeat> 454 <repeat name="tracks">
300 <repeat name="tracks"> 455 <conditional name="track_file_style_conditional">
301 <param name="track_input" value="domains.bed" ftype="bed" /> 456 <param name="track_file_style_selector" value="bedgraph_track_option" />
302 <param name="type" value="vlines"/> 457 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
303 </repeat> 458 <param name="title" value="bedgraph" />
304 <output name="outFileName" file="hicPlotTADs_result1.svg" ftype="svg" compare="sim_size" delta="35000"/> 459 <param name="width_bedgraph" value="4" />
460 <param name="color" value="blue" />
461 </conditional>
462 </repeat>
463 <repeat name="tracks">
464 <conditional name="track_file_style_conditional">
465 <param name="track_file_style_selector" value="bigwig_track_option" />
466 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
467 <param name="title" value="rep 1 test fill" />
468 <param name="width_bigwig" value="4" />
469 <param name="color" value="blue" />
470 <conditional name="type_conditional">
471 <param name="type_selector" value="fill_option" />
472 </conditional>
473 </conditional>
474 </repeat>
475
476 <repeat name="tracks">
477 <conditional name="track_file_style_conditional">
478 <param name="track_file_style_selector" value="bigwig_track_option" />
479 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
480 <param name="title" value="rep 1 test line" />
481 <param name="width_bigwig" value="4" />
482 <param name="color" value="red" />
483 <conditional name="type_conditional">
484 <param name="type_selector" value="line_option" />
485 <param name="width_line" value="1" />
486 </conditional>
487 </conditional>
488 </repeat>
489
490 <repeat name="tracks">
491 <conditional name="track_file_style_conditional">
492 <param name="track_file_style_selector" value="bigwig_track_option" />
493 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
494 <param name="title" value="rep 1 test lw=0.2" />
495 <param name="width_bigwig" value="4" />
496 <param name="color" value="red" />
497 <conditional name="type_conditional">
498 <param name="type_selector" value="line_option" />
499 <param name="width_line" value="0.1" />
500
501 </conditional>
502 </conditional>
503 </repeat>
504
505 <repeat name="tracks">
506 <conditional name="track_file_style_conditional">
507 <param name="track_file_style_selector" value="bigwig_track_option" />
508 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
509 <param name="title" value="rep 1 test point:0.5" />
510 <param name="width_bigwig" value="4" />
511 <param name="color" value="black" />
512 <conditional name="type_conditional">
513 <param name="type_selector" value="point_option" />
514 <param name="width_point" value="0.5" />
515
516 </conditional>
517 </conditional>
518 </repeat>
519
520 <repeat name="tracks">
521 <conditional name="track_file_style_conditional">
522 <param name="track_file_style_selector" value="spacer_option" />
523 <param name="spacer_width" value="0.5" />
524 </conditional>
525 </repeat>
526 <repeat name="tracks">
527 <conditional name="track_file_style_conditional">
528 <param name="track_file_style_selector" value="gene_track_option" />
529 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
530 <param name="title" value="genes" />
531 <param name="width_bed" value="5" />
532 <param name="fontsize" value="10" />
533 </conditional>
534 </repeat>
535 <repeat name="tracks">
536 <conditional name="track_file_style_conditional">
537 <param name="track_file_style_selector" value="spacer_option" />
538 <param name="spacer_width" value="1" />
539 </conditional>
540 </repeat>
541 <repeat name="tracks">
542 <conditional name="track_file_style_conditional">
543 <param name="track_file_style_selector" value="gene_track_option" />
544 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
545 <param name="title" value="max num rows 3" />
546 <param name="width_bed" value="3" />
547 <param name="fontsize" value="8" />
548 <param name="gene_rows" value="3" />
549 </conditional>
550 </repeat>
551 <repeat name="tracks">
552 <conditional name="track_file_style_conditional">
553 <param name="track_file_style_selector" value="spacer_option" />
554 <param name="spacer_width" value="1" />
555 </conditional>
556 </repeat>
557 <repeat name="tracks">
558 <conditional name="track_file_style_conditional">
559 <param name="track_file_style_selector" value="gene_track_option" />
560 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
561 <param name="title" value="bed6 global max row" />
562 <param name="width_bed" value="20" />
563 <param name="fontsize" value="10" />
564 <param name="global_max_row" value="True" />
565 </conditional>
566 </repeat>
567 <repeat name="tracks">
568 <conditional name="track_file_style_conditional">
569 <param name="track_file_style_selector" value="vlines_track_option" />
570 <param name="track_input_bed" value="domains.bed" ftype="bed" />
571 <param name="type" value="vlines" />
572 </conditional>
573 </repeat>
574 <param name="image_file_format" value="png" />
575 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
305 </test> 576 </test>
306 </tests> 577 </tests>
307 <help><![CDATA[ 578 <help><![CDATA[
308 579
309 **What it does** 580 **What it does**
310 581
311 Plots the diagonal, and some values close to the diagonal of a HiC matrix. The diagonal of the matrix is plotted horizontally for a region. 582 Plots the diagonal, and some values close to the diagonal of a Hi-C matrix. The diagonal of the matrix is plotted horizontally for a region.
312 583
313 ]]></help> 584 ]]></help>
314 <expand macro="citations" /> 585 <expand macro="citations" />
315 </tool> 586 </tool>