Mercurial > repos > iuc > pygenometracks

comparison test-data/test3.ini @ 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
children 326a3db8d9d1
comparison
equal deleted inserted replaced
4:c237ba772225 5:eca03db4f612
1 [x-axis]
2 where = top
3 [hic_section_0_0]
4 file = test-data/Li_et_al_2015.h5
5 file_type = hic_matrix
6 title = Kc DpnII (Li et al. 2015) log1p
7 depth = 200000
8 colormap = RdYlBu_r
9 transform = log1p
10 scale_factor = 1.0
11 rasterize = true
12 [tads_0_0]
13 file = test-data/domains.bed
14 file_type = domains
15 border_color = black
16 color = none
17 overlay_previous = share-y
18 [chrom states_1]
19 file = test-data/tad_classification.bed
20 title = TAD state
21 color = bed_rgb
22 border_color = #000000
23 display = collapsed
24 height = 0.5
25 line_width = 0.5
26 file_type = bed
27 [hic_section_2_0]
28 file = test-data/Li_et_al_2015.h5
29 file_type = hic_matrix
30 title = Kc DpnII (Li et al. 2015) inverted no transform
31 depth = 200000
32 colormap = Reds
33 min_value = 5.0
34 max_value = 70.0
35 orientation = inverted
36 scale_factor = 1.0
37 rasterize = true
38 [spacer]
39 height = 1.0
40 [bedgraph_4]
41 file = test-data/test_with_neg_values.bg.gz
42 title = bedgraph with negative values
43 color = black
44 alpha = 1.0
45 negative_color = red
46 height = 4.0
47 show_data_range = false
48 nans_to_zeros = false
49 use_middle = false
50 file_type = bedgraph
51 type = fill
52 overlay_previous = no
53 [bedgraph_5]
54 file = test-data/bedgraph_chrx_2e6_5e6.bg
55 title = bedgraph
56 color = blue
57 alpha = 1.0
58 height = 4.0
59 show_data_range = false
60 nans_to_zeros = false
61 use_middle = false
62 file_type = bedgraph
63 type = fill
64 overlay_previous = no
65 [bigwig_6]
66 file = test-data/bigwig_chrx_2e6_5e6.bw
67 title = rep 1 test fill
68 color = blue
69 alpha = 1.0
70 height = 4.0
71 summary_method = mean
72 nans_to_zeros = false
73 type = fill
74 show_data_range = false
75 file_type = bigwig
76 overlay_previous = no
77 [bigwig_7]
78 file = test-data/bigwig_chrx_2e6_5e6.bw
79 title = (red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)
80 color = red
81 alpha = 1.0
82 height = 10.0
83 summary_method = max
84 nans_to_zeros = false
85 number_of_bins = 100
86 type = points:5.0
87 show_data_range = false
88 file_type = bigwig
89 overlay_previous = no
90 [bigwig_8]
91 file = test-data/bigwig_chrx_2e6_5e6.bw
92 color = #c00000
93 alpha = 1.0
94 height = 10.0
95 summary_method = min
96 nans_to_zeros = false
97 type = line:0.5
98 show_data_range = false
99 file_type = bigwig
100 overlay_previous = share-y
101 [bigwig_9]
102 file = test-data/bigwig_chrx_2e6_5e6.bw
103 color = black
104 alpha = 1.0
105 height = 10.0
106 summary_method = min
107 nans_to_zeros = false
108 number_of_bins = 30000
109 type = line:0.5
110 show_data_range = false
111 file_type = bigwig
112 overlay_previous = share-y
113 [spacer]
114 height = 1.0
115 [genes_10_0]
116 file = test-data/dm3_genes.bed.gz
117 title = genes in ucsc
118 color = #000000
119 border_color = #000000
120 style = UCSC
121 arrow_interval = 2
122 display = stacked
123 height = 5.0
124 labels = true
125 file_type = bed
126 fontsize = 10
127 global_max_row = false
128 max_labels = 60
129 line_width = 0.5
130 arrowhead_included = false
131 overlay_previous = no
132 [genes_11_0]
133 file = test-data/dm3_genes.bed6.gz
134 title = bed6 global max row color from score
135 color = RdYlBu_r
136 border_color = #000000
137 style = flybase
138 height_utr = 1.0
139 color_utr = grey
140 display = stacked
141 height = 20.0
142 labels = true
143 file_type = bed
144 fontsize = 10
145 global_max_row = true
146 max_labels = 60
147 line_width = 0.5
148 arrowhead_included = false
149 overlay_previous = no
150 [genes_12_0]
151 file = test-data/domains.bed
152 title = domains.bed using the 9th field for colors interleaved
153 color = bed_rgb
154 border_color = red
155 style = flybase
156 height_utr = 1.0
157 color_utr = grey
158 display = interleaved
159 height = 2.0
160 labels = false
161 file_type = bed
162 fontsize = 10
163 global_max_row = false
164 max_labels = 60
165 line_width = 0.5
166 arrowhead_included = false
167 overlay_previous = no