# HG changeset patch
# User iuc
# Date 1587139064 14400
# Node ID 326a3db8d9d1e5bc4eaccdd71e7fadee7d8f59da
# Parent 5cec5fb749f0a8bca18a173e28999663da6c376d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit d82c81c0900d94b9363379ed4df9a067a058dbd2"
diff -r 5cec5fb749f0 -r 326a3db8d9d1 macros.xml
--- a/macros.xml Tue Feb 11 10:20:24 2020 -0500
+++ b/macros.xml Fri Apr 17 11:57:44 2020 -0400
@@ -1,6 +1,6 @@
\${GALAXY_SLOTS:-4}
- 3.2.1
+ 3.3
pygenometracks
@@ -15,159 +15,6 @@
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.. class:: infomark
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.. _help site: https://github.com/deeptools/pyGenomeTracks
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diff -r 5cec5fb749f0 -r 326a3db8d9d1 pyGenomeTracks.xml
--- a/pyGenomeTracks.xml Tue Feb 11 10:20:24 2020 -0500
+++ b/pyGenomeTracks.xml Fri Apr 17 11:57:44 2020 -0400
@@ -30,24 +30,20 @@
#if $region and $region is not None:
--region '$region'
#end if
+ #if $global_args.title is not None:
+ --title '$global_args.title'
+ #end if
+ --fontSize $global_args.fontsize
+ --dpi $global_args.dpi
+ --trackLabelFraction $global_args.trackLabelFraction
+ --trackLabelHAlign $global_args.trackLabelHAlign
--outFileName plot.$image_file_format
&& mv plot.$image_file_format plot
]]>
-## First the xaxis if where = top
-#if $x_axis.x_axis_select == "true":
- #if $x_axis.where == 'top':
-[x-axis]
- #if $x_axis.fontsize:
-fontsize = $x_axis.fontsize
- #end if
-where = top
- #end if
-#end if
-
-## Then each track:
+## Each track:
#for $counter, $track in enumerate($tracks):
## Hi-C Track
#if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
@@ -124,8 +120,10 @@
#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
+ #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
+border_color = $track.track_file_style_conditional.border_color_bed.color
+ #else
+border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
#end if
display = collapsed
#if $track.track_file_style_conditional.height_chrom:
@@ -148,8 +146,8 @@
#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
+prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name
+merge_transcripts = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts
#end if
#if $track.track_file_style_conditional.title:
title = $track.track_file_style_conditional.title
@@ -161,33 +159,53 @@
#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
+ #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
+border_color = $track.track_file_style_conditional.border_color_bed.color
+ #else
+border_color = $track.track_file_style_conditional.border_color_bed.border_color_bed_select
#end if
- #if $track.track_file_style_conditional.flybase:
-style = flybase
-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
-arrow_interval = $track.track_file_style_conditional.bed_advanced.ucsc.arrow_interval
+style = $track.track_file_style_conditional.bed_style.bed_style_select
+ #if $track.track_file_style_conditional.bed_style.bed_style_select == 'UCSC':
+arrow_interval = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_interval
+ #else:
+height_utr = $track.track_file_style_conditional.bed_style.bed_advanced.height_utr
+ #if $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'manually':
+color_utr = $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color
+ #elif $track.track_file_style_conditional.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb':
+color_utr = bed_rgb
+ #else:
+ #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
+color_utr = bed_rgb
+ #else:
+color_utr = $track.track_file_style_conditional.color_bed.color
+ #end if
+ #end if
+ #if $track.track_file_style_conditional.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length != '':
+arrow_length = $track.track_file_style_conditional.bed_style.bed_advanced.arrow_length
+ #end if
+ #if $track.track_file_style_conditional.bed_style.bed_style_select == 'flybase':
+arrowhead_included = $track.track_file_style_conditional.bed_style.arrowhead_included
+ #end if
#end if
display = $track.track_file_style_conditional.display
#if $track.track_file_style_conditional.height_bed:
height = $track.track_file_style_conditional.height_bed
#end if
-labels = $track.track_file_style_conditional.labels
+labels = $track.track_file_style_conditional.labels.plot_labels
+ #if $track.track_file_style_conditional.labels.plot_labels == 'true':
+all_labels_inside = $track.track_file_style_conditional.labels.all_labels_inside
+labels_in_margin = $track.track_file_style_conditional.labels.labels_in_margin
+ #end if
file_type = bed
#if $track.track_file_style_conditional.fontsize:
fontsize = $track.track_file_style_conditional.fontsize
#end if
- #if $track.track_file_style_conditional.bed_advanced.gene_rows:
-gene_rows = $track.track_file_style_conditional.bed_advanced.gene_rows
+ #if $track.track_file_style_conditional.bed_style.bed_advanced.gene_rows:
+gene_rows = $track.track_file_style_conditional.bed_style.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
+global_max_row = $track.track_file_style_conditional.bed_style.bed_advanced.global_max_row
+max_labels = $track.track_file_style_conditional.bed_style.bed_advanced.max_labels
+line_width = $track.track_file_style_conditional.bed_style.bed_advanced.line_width
#if $track.track_file_style_conditional.invert_orientation:
orientation = inverted
#end if
@@ -223,6 +241,10 @@
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
+compact_arcs_level = $track.track_file_style_conditional.compact_arcs_level
+ #if $track.track_file_style_conditional.ylim != "":
+ylim = $track.track_file_style_conditional.ylim
+ #end if
#if $track.track_file_style_conditional.invert_orientation:
orientation = inverted
#end if
@@ -263,6 +285,7 @@
#if $track.track_file_style_conditional.height_narrow_peak:
height = $track.track_file_style_conditional.height_narrow_peak
#end if
+line_width = $track.track_file_style_conditional.line_width
show_labels = $track.track_file_style_conditional.show_labels
file_type = narrow_peak
#if $track.track_file_style_conditional.fontsize:
@@ -404,13 +427,15 @@
#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:
-type = $track.track_file_style_conditional.type_lines
- #end if
+type = $track.track_file_style_conditional.type.type_selector
file_type = bedgraph_matrix
-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.type.type_selector == 'lines':
+show_data_range = $track.track_file_style_conditional.type.show_data
+plot_horizontal_lines = $track.track_file_style_conditional.type.plot_horizontal_lines
+pos_score_in_bin = $track.track_file_style_conditional.type.pos_score_in_bin
+ #else
+colormap = $track.track_file_style_conditional.type.colormap
+ #end if
#if $track.track_file_style_conditional.invert_orientation:
orientation = inverted
#end if
@@ -465,28 +490,83 @@
## Spacer
#if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
[spacer]
+ #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+ #end if
#if $track.track_file_style_conditional.spacer_height != "":
height = $track.track_file_style_conditional.spacer_height
#end if
#end if
+
+ ## Xaxis:
+ #if $track.track_file_style_conditional.track_file_style_selector == "xaxis_option":
+[x-axis]
+ #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+ #end if
+ #if $track.track_file_style_conditional.fontsize != "":
+fontsize = $track.track_file_style_conditional.fontsize
+ #end if
+where = $track.track_file_style_conditional.xaxis_where
+ ## 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
+
+ ## Scale bar:
+ #if $track.track_file_style_conditional.track_file_style_selector == "scale_bar_option":
+[scale_bar]
+ #if $track.track_file_style_conditional.title:
+title = $track.track_file_style_conditional.title
+ #end if
+ #if $track.track_file_style_conditional.color != "":
+color = $track.track_file_style_conditional.color
+ #end if
+alpha = $track.track_file_style_conditional.alpha
+line_width = $track.track_file_style_conditional.line_width
+ #if $track.track_file_style_conditional.x_center != "":
+x_center = $track.track_file_style_conditional.x_center
+ #end if
+ #if $track.track_file_style_conditional.size != "":
+size = $track.track_file_style_conditional.size
+ #end if
+where = $track.track_file_style_conditional.sb_where
+ #if $track.track_file_style_conditional.fontsize != "":
+fontsize = $track.track_file_style_conditional.fontsize
+ #end if
+file_type = scalebar
+ ## 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 for
-
-#if $x_axis.x_axis_select == "true":
- #if $x_axis.where == 'bottom':
-[x-axis]
- #if $x_axis.fontsize:
-fontsize = $x_axis.fontsize
- #end if
-where = bottom
- #end if
-#end if
-
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+ help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph.
+ The order you add them represent the order they will be plotted from top to bottom.">
@@ -501,12 +581,17 @@
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optional="True" label="Plot a vertical bar at the summit position." />
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