# HG changeset patch
# User iuc
# Date 1578492919 18000
# Node ID eca03db4f61207667a629801633f420c40cf813d
# Parent c237ba7722252b4fb2af8fff1bceadeb36fa5a57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9471ad965cd7c88c96a03c97fc1cdfe17f379c95"
diff -r c237ba772225 -r eca03db4f612 macros.xml
--- a/macros.xml Thu Sep 19 17:18:54 2019 -0400
+++ b/macros.xml Wed Jan 08 09:15:19 2020 -0500
@@ -1,10 +1,9 @@
\${GALAXY_SLOTS:-4}
- 3.1.1
+ 3.2.1
pygenometracks
-
@@ -165,8 +164,8 @@
help="The format is chr:start-end. Also valid is just to specify a chromosome, for example chr10:10-500" />
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diff -r c237ba772225 -r eca03db4f612 pyGenomeTracks.xml
--- a/pyGenomeTracks.xml Thu Sep 19 17:18:54 2019 -0400
+++ b/pyGenomeTracks.xml Wed Jan 08 09:15:19 2020 -0500
@@ -1,4 +1,4 @@
-
+
plot genomic data tracks
pyGenomeTracks
@@ -7,6 +7,7 @@
-#if $x_axis.x_axis_select == "yes":
-#if $x_axis.where == 'top':
+## First the xaxis if where = top
+#if $x_axis.x_axis_select == "true":
+ #if $x_axis.where == 'top':
[x-axis]
-#if $x_axis.fontsize:
+ #if $x_axis.fontsize:
fontsize = $x_axis.fontsize
-#end if
-#if $x_axis.where:
-where = $x_axis.where
+ #end if
+where = top
+ #end if
#end if
-#end if
-#end if
+
+## Then each track:
#for $counter, $track in enumerate($tracks):
-#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
-
-#for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
+ ## Hi-C Track
+ #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
+ #for $counter_matrix, $data_matrix in enumerate($track.track_file_style_conditional.matrix_h5_cooler_multiple):
[hic_section_${counter}_${counter_matrix}]
-#set ext = $data_matrix.extension
+ #set ext = $data_matrix.extension
file = ${counter}_${counter_matrix}.$ext
file_type = hic_matrix
-#if $track.track_file_style_conditional.title:
+ #if $track.track_file_style_conditional.title:
title = $track.track_file_style_conditional.title
-#else:
+ #else:
title = $data_matrix.name
-#end if
-#if $track.track_file_style_conditional.depth:
+ #end if
+ #if $track.track_file_style_conditional.depth:
depth = $track.track_file_style_conditional.depth
-#end if
-#if $track.track_file_style_conditional.colormap:
+ #end if
+ #if $track.track_file_style_conditional.colormap:
colormap = $track.track_file_style_conditional.colormap
-#end if
-#if $track.track_file_style_conditional.min_value:
+ #end if
+ #if $track.track_file_style_conditional.min_value:
min_value = $track.track_file_style_conditional.min_value
-#end if
-#if $track.track_file_style_conditional.max_value:
+ #end if
+ #if $track.track_file_style_conditional.max_value:
max_value = $track.track_file_style_conditional.max_value
-#end if
-#if $track.track_file_style_conditional.transform != "":
+ #end if
transform = $track.track_file_style_conditional.transform
-#end if
-#if $track.track_file_style_conditional.height_matrix != "":
+ #if $track.track_file_style_conditional.height_matrix != "":
height = $track.track_file_style_conditional.height_matrix
-#end if
-
-#if $track.track_file_style_conditional.show_masked_bins:
+ #end if
+ #if $track.track_file_style_conditional.show_masked_bins:
show_masked_bins = $track.track_file_style_conditional.show_masked_bins
-#end if
-#if $track.track_file_style_conditional.invert_orientation:
+ #end if
+ #if $track.track_file_style_conditional.invert_orientation:
orientation = inverted
-#end if
-#if $track.track_file_style_conditional.scale_factor:
-scale factor = $track.track_file_style_conditional.scale_factor
-#end if
-
-#if str($track.track_file_style_conditional.boundaries_file) != "None":
-#if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
-#set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
-#else:
-#set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
-#end if
+ #end if
+ #if $track.track_file_style_conditional.scale_factor:
+scale_factor = $track.track_file_style_conditional.scale_factor
+ #end if
+rasterize = $track.track_file_style_conditional.rasterize
+ ## If a boundary file is given a new section needs to be written:
+ #if str($track.track_file_style_conditional.boundaries_file) != "None":
+ #if len($track.track_file_style_conditional.boundaries_file)>$counter_matrix:
+ #set boundary_file = $track.track_file_style_conditional.boundaries_file[$counter_matrix]
+ #else:
+ #set boundary_file = $track.track_file_style_conditional.boundaries_file[0]
+ #end if
[tads_${counter}_${counter_matrix}]
file = $boundary_file
file_type = domains
-border color = black
+border_color = black
color = none
-overlay previous = share-y
-#end if
-
-
-#if $track.track_file_style_conditional.spacer_height != "":
+overlay_previous = share-y
+ #end if
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
[spacer]
height = $track.track_file_style_conditional.spacer_height
-#end if
-#end for
-
-#end if
-
-
-
-#if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
+ #end if
+ #end for
+ #end if
-#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
-[tad_score_$counter]
-file = $data_bedgraph
-#if $track.track_file_style_conditional.title:
-title = $track.track_file_style_conditional.title
-#else:
-title = $data_bedgraph.name
-#end if
-#if $track.track_file_style_conditional.color:
-color = $track.track_file_style_conditional.color
-#end if
-#if $track.track_file_style_conditional.height_tad:
-height = $track.track_file_style_conditional.height_tad
-#end if
-show data range = $track.track_file_style_conditional.show_data
-
-#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
-#if $columns > 4:
-file_type = bedgraph_matrix
-#if $track.track_file_style_conditional.type_lines:
-type = $track.track_file_style_conditional.type_lines
-#end if
-#else:
-file_type = bedgraph
-#end if
-#if $track.track_file_style_conditional.spacer_height != "":
-[spacer]
-height = $track.track_file_style_conditional.spacer_height
-#end if
-#end for
-#end if
-
-
-
-
-#if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
-#for $data_bed in $track.track_file_style_conditional.track_input_bed:
-
+ ## Chrom_state track
+ #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
+ #for $data_bed in $track.track_file_style_conditional.track_input_bed:
[chrom states_$counter]
file = $data_bed
-#if $track.track_file_style_conditional.title:
+ #if $track.track_file_style_conditional.title:
title = $track.track_file_style_conditional.title
-#else:
+ #else:
title = $data_bed.name
-#end if
-#if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
+ #end if
+ #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
color = bed_rgb
-#elif $track.track_file_style_conditional.color_bed.color:
+ #elif $track.track_file_style_conditional.color_bed.color:
color = $track.track_file_style_conditional.color_bed.color
-#end if
-#if $track.track_file_style_conditional.border_color:
-border color = $track.track_file_style_conditional.border_color
-#end if
+ #end if
+ #if $track.track_file_style_conditional.border_color:
+border_color = $track.track_file_style_conditional.border_color
+ #end if
display = collapsed
-#if $track.track_file_style_conditional.height_chrom:
+ #if $track.track_file_style_conditional.height_chrom:
height = $track.track_file_style_conditional.height_chrom
-#end if
+ #end if
+line_width = $track.track_file_style_conditional.line_width
file_type = bed
-#if $track.track_file_style_conditional.spacer_height != "":
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
[spacer]
height = $track.track_file_style_conditional.spacer_height
-#end if
-#end for
-
-#end if
-
-
-
-
-#if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
-#for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
-
-[genes_${counter}_${counter_bed}]
-#set ext = $data_bed.extension
-file = ${counter}_${counter_bed}.$ext
-#if $track.track_file_style_conditional.title:
-title = $track.track_file_style_conditional.title
-#else:
-title = $data_bed.name
-#end if
-#if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
-color = bed_rgb
-#elif $track.track_file_style_conditional.color_bed.color:
-color = $track.track_file_style_conditional.color_bed.color
-#end if
-#if $track.track_file_style_conditional.border_color:
-border color = $track.track_file_style_conditional.border_color
-#end if
+ #end if
+ #end for
+ #end if
-#if $track.track_file_style_conditional.flybase:
+ ## Gene/gtf track
+ #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
+ #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
+[genes_${counter}_${counter_bed}]
+ #set ext = $data_bed.extension
+file = ${counter}_${counter_bed}.$ext
+ #if $ext == 'gtf':
+prefered_name = $track.track_file_style_conditional.bed_advanced.gtf.prefered_name
+merge_transcripts = $track.track_file_style_conditional.bed_advanced.gtf.merge_transcripts
+ #end if
+ #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+ #elif $track.track_file_style_conditional.overlay_select == 'no':
+title = $data_bed.name
+ #end if
+ #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
+color = bed_rgb
+ #elif $track.track_file_style_conditional.color_bed.color:
+color = $track.track_file_style_conditional.color_bed.color
+ #end if
+ #if $track.track_file_style_conditional.border_color:
+border_color = $track.track_file_style_conditional.border_color
+ #end if
+ #if $track.track_file_style_conditional.flybase:
style = flybase
-#else
+height_utr = $track.track_file_style_conditional.bed_advanced.flybase.height_utr
+color_utr = $track.track_file_style_conditional.bed_advanced.flybase.color_utr
+ #else
style = UCSC
-#end if
-
+arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval
+ #end if
display = $track.track_file_style_conditional.display
-
-#if $track.track_file_style_conditional.height_bed:
+ #if $track.track_file_style_conditional.height_bed:
height = $track.track_file_style_conditional.height_bed
-#end if
-
+ #end if
labels = $track.track_file_style_conditional.labels
-
file_type = bed
-#if $track.track_file_style_conditional.fontsize:
+ #if $track.track_file_style_conditional.fontsize:
fontsize = $track.track_file_style_conditional.fontsize
-#end if
-
-#if $track.track_file_style_conditional.gene_rows:
-gene rows = $track.track_file_style_conditional.gene_rows
-#end if
-
-#if $track.track_file_style_conditional.global_max_row:
-global max row = $track.track_file_style_conditional.global_max_row
-#end if
-#if $track.track_file_style_conditional.spacer_height != "":
+ #end if
+ #if $track.track_file_style_conditional.bed_advanced.gene_rows:
+gene_rows = $track.track_file_style_conditional.bed_advanced.gene_rows
+ #end if
+global_max_row = $track.track_file_style_conditional.bed_advanced.global_max_row
+max_labels = $track.track_file_style_conditional.bed_advanced.max_labels
+line_width = $track.track_file_style_conditional.bed_advanced.line_width
+arrowhead_included = $track.track_file_style_conditional.arrowhead_included
+ #if $track.track_file_style_conditional.invert_orientation:
+orientation = inverted
+ #end if
+overlay_previous = $track.track_file_style_conditional.overlay_select
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
[spacer]
height = $track.track_file_style_conditional.spacer_height
-#end if
-#end for
-#end if
+ #end if
+ #end for
+ #end if
-#if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option":
-#for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak):
+ ## Link
+ #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option":
+[links_$counter]
+file = $track.track_file_style_conditional.track_input_link
+ #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+ #elif $track.track_file_style_conditional.overlay_select == 'no':
+title = $track.track_file_style_conditional.track_input_link.name
+ #end if
+ #if $track.track_file_style_conditional.height:
+height = $track.track_file_style_conditional.height
+ #end if
+ #if $track.track_file_style_conditional.min_value:
+min_value = $track.track_file_style_conditional.min_value
+ #end if
+ #if $track.track_file_style_conditional.max_value:
+max_value = $track.track_file_style_conditional.max_value
+ #end if
+color = $track.track_file_style_conditional.color_link.color
+alpha = $track.track_file_style_conditional.alpha
+line_width = $track.track_file_style_conditional.line_width
+line_style = $track.track_file_style_conditional.line_style
+links_type = $track.track_file_style_conditional.links_type
+ #if $track.track_file_style_conditional.invert_orientation:
+orientation = inverted
+ #end if
+overlay_previous = $track.track_file_style_conditional.overlay_select
+file_type = links
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
+[spacer]
+height = $track.track_file_style_conditional.spacer_height
+ #end if
+ #end if
+ ## Narrow peak
+ #if $track.track_file_style_conditional.track_file_style_selector == "narrow_peak_track_option":
+ #for $counter_narrow_peak, $data_narrow_peak in enumerate($track.track_file_style_conditional.track_input_narrow_peak):
[narrow_peak_${counter}_${counter_narrow_peak}]
file = $data_narrow_peak
-#if $track.track_file_style_conditional.title:
+ #if $track.track_file_style_conditional.title:
title = $track.track_file_style_conditional.title
-#else:
+ #elif $track.track_file_style_conditional.overlay_select == 'no':
title = $data_narrow_peak.name
-#end if
+ #end if
color = $track.track_file_style_conditional.color
type = $track.track_file_style_conditional.display.display_selector
-use summit = $track.track_file_style_conditional.display.use_summit
-#if $track.track_file_style_conditional.display.display_selector == "peak":
-show data range = $track.track_file_style_conditional.display.show_data
-#if $track.track_file_style_conditional.display.width_adjust:
-width adjust = $track.track_file_style_conditional.display.width_adjust
-#end if
-#if $track.track_file_style_conditional.display.min_value:
+use_summit = $track.track_file_style_conditional.display.use_summit
+ #if $track.track_file_style_conditional.display.display_selector == "peak":
+show_data_range = $track.track_file_style_conditional.display.show_data
+ #if $track.track_file_style_conditional.display.width_adjust:
+width_adjust = $track.track_file_style_conditional.display.width_adjust
+ #end if
+ #if $track.track_file_style_conditional.display.min_value:
min_value = $track.track_file_style_conditional.display.min_value
-#end if
-#if $track.track_file_style_conditional.display.max_value:
+ #end if
+ #if $track.track_file_style_conditional.display.max_value:
max_value = $track.track_file_style_conditional.display.max_value
-#end if
-#end if
-
-
-#if $track.track_file_style_conditional.height_narrow_peak:
+ #end if
+ #end if
+ #if $track.track_file_style_conditional.height_narrow_peak:
height = $track.track_file_style_conditional.height_narrow_peak
-#end if
-
-show labels = $track.track_file_style_conditional.show_labels
-
+ #end if
+show_labels = $track.track_file_style_conditional.show_labels
file_type = narrow_peak
-#if $track.track_file_style_conditional.fontsize:
+ #if $track.track_file_style_conditional.fontsize:
fontsize = $track.track_file_style_conditional.fontsize
-#end if
-
-#if $track.track_file_style_conditional.spacer_height != "":
+ #end if
+ #if $track.track_file_style_conditional.invert_orientation:
+orientation = inverted
+ #end if
+overlay_previous = $track.track_file_style_conditional.overlay_select
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
[spacer]
height = $track.track_file_style_conditional.spacer_height
-#end if
-#end for
-#end if
+ #end if
+ #end for
+ #end if
-
-#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
-#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
-
+ ## Bedgraph track
+ #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
+ #for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
[bedgraph_$counter]
file = $data_bedgraph
-#if $track.track_file_style_conditional.title:
+ #if $track.track_file_style_conditional.title:
title = $track.track_file_style_conditional.title
-#elif $track.track_file_style_conditional.overlay_select == "no":
+ #elif $track.track_file_style_conditional.overlay_select == "no":
title = $data_bedgraph.name
-#end if
-#if $track.track_file_style_conditional.color:
+ #end if
+ #if $track.track_file_style_conditional.color:
color = $track.track_file_style_conditional.color
-#end if
+ #end if
alpha = $track.track_file_style_conditional.alpha
-#if $track.track_file_style_conditional.color_negative.color_negative_select == "yes":
-negative color = $track.track_file_style_conditional.color_negative.color
-#end if
-#if $track.track_file_style_conditional.height_bedgraph:
+ #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
+negative_color = $track.track_file_style_conditional.color_negative.color
+ #end if
+ #if $track.track_file_style_conditional.height_bedgraph:
height = $track.track_file_style_conditional.height_bedgraph
-#end if
-#if $track.track_file_style_conditional.min_value:
+ #end if
+ #if $track.track_file_style_conditional.min_value:
min_value = $track.track_file_style_conditional.min_value
-#else:
-min_value = auto
-#end if
-#if $track.track_file_style_conditional.max_value:
+ #end if
+ #if $track.track_file_style_conditional.max_value:
max_value = $track.track_file_style_conditional.max_value
-#else:
-max_value = auto
-#end if
-
-show data range = $track.track_file_style_conditional.show_data
-
-#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
-#if $columns > 4:
+ #end if
+show_data_range = $track.track_file_style_conditional.show_data
+nans_to_zeros = $track.track_file_style_conditional.nans_to_zeros
+use_middle = $track.track_file_style_conditional.use_middle
+ #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
+ #if $columns > 4:
file_type = bedgraph_matrix
type = lines
-#else:
+ #else:
file_type = bedgraph
-#if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
+ #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
type = fill
-#elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
+ #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
type = line:$track.track_file_style_conditional.type_conditional.width_line
-#elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
+ #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
type = points:$track.track_file_style_conditional.type_conditional.width_point
-#end if
-#end if
-#if $track.track_file_style_conditional.invert_orientation:
+ #end if
+ #end if
+ #if $track.track_file_style_conditional.invert_orientation:
orientation = inverted
-#end if
-overlay previous = $track.track_file_style_conditional.overlay_select
-#if $track.track_file_style_conditional.spacer_height != "":
+ #end if
+overlay_previous = $track.track_file_style_conditional.overlay_select
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
[spacer]
height = $track.track_file_style_conditional.spacer_height
-#end if
-#end for
-#end if
+ #end if
+ #end for
+ #end if
-#if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
-#for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
+ ## Bigwig tracks
+ #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
+ #for $data_bigwig in $track.track_file_style_conditional.track_input_bigwig:
[bigwig_$counter]
file = $data_bigwig
-#if $track.track_file_style_conditional.title:
+ #if $track.track_file_style_conditional.title:
title = $track.track_file_style_conditional.title
-#elif $track.track_file_style_conditional.overlay_select == "no":
+ #elif $track.track_file_style_conditional.overlay_select == "no":
title = $data_bigwig.name
-#end if
-#if $track.track_file_style_conditional.color:
+ #end if
+ #if $track.track_file_style_conditional.color:
color = $track.track_file_style_conditional.color
-#end if
+ #end if
alpha = $track.track_file_style_conditional.alpha
-#if $track.track_file_style_conditional.color_negative.color_negative_select == "yes":
-negative color = $track.track_file_style_conditional.color_negative.color
-#end if
-#if $track.track_file_style_conditional.min_value:
+ #if $track.track_file_style_conditional.color_negative.color_negative_select == "true":
+negative_color = $track.track_file_style_conditional.color_negative.color
+ #end if
+ #if $track.track_file_style_conditional.min_value:
min_value = $track.track_file_style_conditional.min_value
-#else:
-min_value = 0
-#end if
-#if $track.track_file_style_conditional.max_value:
+ #end if
+ #if $track.track_file_style_conditional.max_value:
max_value = $track.track_file_style_conditional.max_value
-#else:
-max_value = auto
-#end if
+ #end if
height = $track.track_file_style_conditional.height_bigwig
-summary method = $track.track_file_style_conditional.reading_bw_conditional.summary
-nans to zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
-#if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
-number of bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
-#end if
-#if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
+summary_method = $track.track_file_style_conditional.reading_bw_conditional.summary
+nans_to_zeros = $track.track_file_style_conditional.reading_bw_conditional.nans_to_zeros
+ #if $track.track_file_style_conditional.reading_bw_conditional.number_of_bins:
+number_of_bins = $track.track_file_style_conditional.reading_bw_conditional.number_of_bins
+ #end if
+ #if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
type = fill
-#elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
+ #elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
type = line:$track.track_file_style_conditional.type_conditional.width_line
-#elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
+ #elif $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
type = points:$track.track_file_style_conditional.type_conditional.width_point
-#end if
-show data range = $track.track_file_style_conditional.show_data
+ #end if
+show_data_range = $track.track_file_style_conditional.show_data
file_type = bigwig
-#if $track.track_file_style_conditional.invert_orientation:
+ #if $track.track_file_style_conditional.invert_orientation:
orientation = inverted
-#end if
-overlay previous = $track.track_file_style_conditional.overlay_select
-#if $track.track_file_style_conditional.spacer_height != "":
+ #end if
+overlay_previous = $track.track_file_style_conditional.overlay_select
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
[spacer]
height = $track.track_file_style_conditional.spacer_height
-#end if
-#end for
-#end if
+ #end if
+ #end for
+ #end if
-
-#if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
-#for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
-
+ ## bedgraph_matrix
+ #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
+ #for $data_bedgraph_matrix in $track.track_file_style_conditional.track_input_bedgraph_matrix:
[bedgraph_matrix_$counter]
file = $data_bedgraph_matrix
-#if $track.track_file_style_conditional.title:
+ #if $track.track_file_style_conditional.title:
title = $track.track_file_style_conditional.title
-#else:
+ #else:
title = $data_bedgraph_matrix.name
-#end if
-#if $track.track_file_style_conditional.height_bedgraph:
+ #end if
+ #if $track.track_file_style_conditional.height_bedgraph:
height = $track.track_file_style_conditional.height_bedgraph
-#end if
-orientation = inverted
-#if $track.track_file_style_conditional.min_value:
+ #end if
+ #if $track.track_file_style_conditional.min_value:
min_value = $track.track_file_style_conditional.min_value
-#end if
-#if $track.track_file_style_conditional.max_value:
+ #end if
+ #if $track.track_file_style_conditional.max_value:
max_value = $track.track_file_style_conditional.max_value
-#end if
-#if $track.track_file_style_conditional.type_lines:
+ #end if
+ #if $track.track_file_style_conditional.type_lines:
type = $track.track_file_style_conditional.type_lines
-#end if
+ #end if
file_type = bedgraph_matrix
-plot horizontal lines=False
-#if $track.track_file_style_conditional.invert_orientation:
+show_data_range = $track.track_file_style_conditional.show_data
+plot_horizontal_lines = $track.track_file_style_conditional.plot_horizontal_lines
+pos_score_in_bin = $track.track_file_style_conditional.pos_score_in_bin
+ #if $track.track_file_style_conditional.invert_orientation:
orientation = inverted
-#end if
-#if $track.track_file_style_conditional.spacer_height != "":
+ #end if
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
[spacer]
height = $track.track_file_style_conditional.spacer_height
-#end if
-#end for
-#end if
+ #end if
+ #end for
+ #end if
-#if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
-
+ ## Vlines:
+ #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
[vlines_$counter]
file = $track.track_file_style_conditional.track_input_bed_single
type = vlines
-file_type = bed
-#end if
-#if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
+ #end if
-#if $track.track_file_style_conditional.spacer_height != "":
+ ## Hlines:
+ #if $track.track_file_style_conditional.track_file_style_selector == "hlines_track_option":
+[hlines_$counter]
+ #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+ #end if
+ #if $track.track_file_style_conditional.height:
+height = $track.track_file_style_conditional.height
+ #end if
+ #if $track.track_file_style_conditional.min_value:
+min_value = $track.track_file_style_conditional.min_value
+ #end if
+ #if $track.track_file_style_conditional.max_value:
+max_value = $track.track_file_style_conditional.max_value
+ #end if
+y_values = $track.track_file_style_conditional.y_values
+show_data_range = $track.track_file_style_conditional.show_data
+color = $track.track_file_style_conditional.color
+alpha = $track.track_file_style_conditional.alpha
+line_width = $track.track_file_style_conditional.line_width
+line_style = $track.track_file_style_conditional.line_style
+ #if $track.track_file_style_conditional.invert_orientation:
+orientation = inverted
+ #end if
+overlay_previous = $track.track_file_style_conditional.overlay_select
+file_type = hlines
+ ## If spacer is asked a new section is created:
+ #if $track.track_file_style_conditional.spacer_height != "":
[spacer]
height = $track.track_file_style_conditional.spacer_height
-#end if
-#end if
+ #end if
+ #end if
+
+ ## Spacer
+ #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
+[spacer]
+ #if $track.track_file_style_conditional.spacer_height != "":
+height = $track.track_file_style_conditional.spacer_height
+ #end if
+ #end if
#end for
-#if $x_axis.x_axis_select == "yes":
-#if $x_axis.where == 'bottom':
+#if $x_axis.x_axis_select == "true":
+ #if $x_axis.where == 'bottom':
[x-axis]
-#if $x_axis.fontsize:
+ #if $x_axis.fontsize:
fontsize = $x_axis.fontsize
-#end if
-#if $x_axis.where:
-where = $x_axis.where
-#end if
-#end if
+ #end if
+where = bottom
+ #end if
#end if
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