annotate test-data/test3.ini @ 5:eca03db4f612 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"

[x-axis]
where = top
[hic_section_0_0]
file = test-data/Li_et_al_2015.h5
file_type = hic_matrix
title = Kc DpnII (Li et al. 2015) log1p
depth = 200000
colormap = RdYlBu_r
transform = log1p
scale_factor = 1.0
rasterize = true
[tads_0_0]
file = test-data/domains.bed
file_type = domains
border_color = black
color = none
overlay_previous = share-y
[chrom states_1]
file = test-data/tad_classification.bed
title = TAD state
color = bed_rgb
border_color = #000000
display = collapsed
height = 0.5
line_width = 0.5
file_type = bed
[hic_section_2_0]
file = test-data/Li_et_al_2015.h5
file_type = hic_matrix
title = Kc DpnII (Li et al. 2015) inverted no transform
depth = 200000
colormap = Reds
min_value = 5.0
max_value = 70.0
orientation = inverted
scale_factor = 1.0
rasterize = true
[spacer]
height = 1.0
[bedgraph_4]
file = test-data/test_with_neg_values.bg.gz
title = bedgraph with negative values
color = black
alpha = 1.0
negative_color = red
height = 4.0
show_data_range = false
nans_to_zeros = false
use_middle = false
file_type = bedgraph
type = fill
overlay_previous = no
[bedgraph_5]
file = test-data/bedgraph_chrx_2e6_5e6.bg
title = bedgraph
color = blue
alpha = 1.0
height = 4.0
show_data_range = false
nans_to_zeros = false
use_middle = false
file_type = bedgraph
type = fill
overlay_previous = no
[bigwig_6]
file = test-data/bigwig_chrx_2e6_5e6.bw
title = rep 1 test fill
color = blue
alpha = 1.0
height = 4.0
summary_method = mean
nans_to_zeros = false
type = fill
show_data_range = false
file_type = bigwig
overlay_previous = no
[bigwig_7]
file = test-data/bigwig_chrx_2e6_5e6.bw
title = (red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)
color = red
alpha = 1.0
height = 10.0
summary_method = max
nans_to_zeros = false
number_of_bins = 100
type = points:5.0
show_data_range = false
file_type = bigwig
overlay_previous = no
[bigwig_8]
file = test-data/bigwig_chrx_2e6_5e6.bw
color = #c00000
alpha = 1.0
height = 10.0
summary_method = min
nans_to_zeros = false
type = line:0.5
show_data_range = false
file_type = bigwig
overlay_previous = share-y
[bigwig_9]
file = test-data/bigwig_chrx_2e6_5e6.bw
color = black
alpha = 1.0
height = 10.0
summary_method = min
nans_to_zeros = false
number_of_bins = 30000
type = line:0.5
show_data_range = false
file_type = bigwig
overlay_previous = share-y
[spacer]
height = 1.0
[genes_10_0]
file = test-data/dm3_genes.bed.gz
title = genes in ucsc
color = #000000
border_color = #000000
style = UCSC
arrow_interval = 2
display = stacked
height = 5.0
labels = true
file_type = bed
fontsize = 10
global_max_row = false
max_labels = 60
line_width = 0.5
arrowhead_included = false
overlay_previous = no
[genes_11_0]
file = test-data/dm3_genes.bed6.gz
title = bed6 global max row color from score
color = RdYlBu_r
border_color = #000000
style = flybase
height_utr = 1.0
color_utr = grey
display = stacked
height = 20.0
labels = true
file_type = bed
fontsize = 10
global_max_row = true
max_labels = 60
line_width = 0.5
arrowhead_included = false
overlay_previous = no
[genes_12_0]
file = test-data/domains.bed
title = domains.bed using the 9th field for colors interleaved
color = bed_rgb
border_color = red
style = flybase
height_utr = 1.0
color_utr = grey
display = interleaved
height = 2.0
labels = false
file_type = bed
fontsize = 10
global_max_row = false
max_labels = 60
line_width = 0.5
arrowhead_included = false
overlay_previous = no