# HG changeset patch
# User iuc
# Date 1566559460 14400
# Node ID c171f2b7d76ee3ef95a99b3b5b96890781f6752d
# Parent 0ea86f6bf2a1972635a8faa6cc9f45cccd8cd1ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 11b5b3cc8b846cc75623a3ef265afe8c68747f2e"
diff -r 0ea86f6bf2a1 -r c171f2b7d76e macros.xml
--- a/macros.xml Mon Jul 02 19:32:13 2018 -0400
+++ b/macros.xml Fri Aug 23 07:24:20 2019 -0400
@@ -1,12 +1,13 @@
\${GALAXY_SLOTS:-4}
- 2.0
+ 3.1
pygenometracks
+
- @BINARY@ --version
+
@@ -188,6 +189,9 @@
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diff -r 0ea86f6bf2a1 -r c171f2b7d76e pyGenomeTracks.xml
--- a/pyGenomeTracks.xml Mon Jul 02 19:32:13 2018 -0400
+++ b/pyGenomeTracks.xml Fri Aug 23 07:24:20 2019 -0400
@@ -7,6 +7,21 @@
$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
+color = none
+overlay previous = share-y
+#end if
+
+
+#if $track.track_file_style_conditional.spacer_height != "":
[spacer]
-#if $track.track_file_style_conditional.spacer_height:
height = $track.track_file_style_conditional.spacer_height
#end if
#end for
@@ -90,7 +117,7 @@
#for $data_bedgraph in $track.track_file_style_conditional.track_input_bedgraph:
[tad_score_$counter]
-file = $data_bedgraph
+file = $data_bedgraph
#if $track.track_file_style_conditional.title:
title = $track.track_file_style_conditional.title
#else:
@@ -102,22 +129,21 @@
#if $track.track_file_style_conditional.height_tad:
height = $track.track_file_style_conditional.height_tad
#end if
-#if $track.track_file_style_conditional.type_lines:
-type = $track.track_file_style_conditional.type_lines
-#end if
#if $track.track_file_style_conditional.show_data:
show data range = $track.track_file_style_conditional.show_data
#end if
#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
-#if $columns > 5:
+#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
-type = lines
+#if $track.track_file_style_conditional.spacer_height != "":
[spacer]
-#if $track.track_file_style_conditional.spacer_height:
height = $track.track_file_style_conditional.spacer_height
#end if
#end for
@@ -136,19 +162,21 @@
#else:
title = $data_bed.name
#end if
-#if $track.track_file_style_conditional.color:
-color = $track.track_file_style_conditional.color
+#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
display = collapsed
#if $track.track_file_style_conditional.height_chrom:
height = $track.track_file_style_conditional.height_chrom
#end if
-#if $track.track_file_style_conditional.border_color:
-border_color = $track.track_file_style_conditional.border_color
-#end if
file_type = bed
+#if $track.track_file_style_conditional.spacer_height != "":
[spacer]
-#if $track.track_file_style_conditional.spacer_height:
height = $track.track_file_style_conditional.spacer_height
#end if
#end for
@@ -159,19 +187,33 @@
#if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
-#for $data_bed in $track.track_file_style_conditional.track_input_bed:
+#for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.track_input_bed):
-[genes_$counter]
-file = $data_bed
+[genes_${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:
-color = $track.track_file_style_conditional.color
+#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
+style = UCSC
+#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
@@ -180,10 +222,6 @@
labels = $track.track_file_style_conditional.labels
#end if
-#if $track.track_file_style_conditional.type:
-type = $track.track_file_style_conditional.type
-#end if
-
file_type = bed
#if $track.track_file_style_conditional.fontsize:
fontsize = $track.track_file_style_conditional.fontsize
@@ -196,8 +234,8 @@
#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 != "":
[spacer]
-#if $track.track_file_style_conditional.spacer_height:
height = $track.track_file_style_conditional.spacer_height
#end if
#end for
@@ -211,28 +249,54 @@
file = $data_bedgraph
#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_bedgraph.name
#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
+#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:
height = $track.track_file_style_conditional.height_bedgraph
#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:
+max_value = $track.track_file_style_conditional.max_value
+#else:
+max_value = auto
+#end if
+
#if $track.track_file_style_conditional.show_data:
show data range = $track.track_file_style_conditional.show_data
#end if
#set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
-#if $columns > 5:
+#if $columns > 4:
file_type = bedgraph_matrix
+type = lines
#else:
file_type = bedgraph
+#if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
+type = fill
+#elif $track.track_file_style_conditional.type_conditional.type_selector == 'line_option':
+type = line:$track.track_file_style_conditional.type_conditional.width_line
+#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
-type = lines
+#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 != "":
[spacer]
-#if $track.track_file_style_conditional.spacer_height:
height = $track.track_file_style_conditional.spacer_height
#end if
#end for
@@ -244,10 +308,16 @@
file = $data_bigwig
#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_bigwig.name
#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
+#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:
min_value = $track.track_file_style_conditional.min_value
#else:
@@ -259,23 +329,28 @@
max_value = auto
#end if
height = $track.track_file_style_conditional.height_bigwig
-#if $track.track_file_style_conditional.number_of_bins:
-number of bins = $track.track_file_style_conditional.number_of_bins
+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
-nans to zeros = $track.track_file_style_conditional.nans_to_zeros
-#if $track.track_file_style_conditional.type_conditional == 'fill_option':
+#if $track.track_file_style_conditional.type_conditional.type_selector == 'fill_option':
type = fill
-#elif $track.track_file_style_conditional.type_conditional == 'line_option':
-type = line:$track.track_file_style_conditional.type_conditional.height_line
-#elif $track.track_file_style_conditional.type_conditional == 'point_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 $track.track_file_style_conditional.type_conditional.type_selector == 'point_option':
type = points:$track.track_file_style_conditional.type_conditional.width_point
#end if
#if $track.track_file_style_conditional.data_range:
show data range = $track.track_file_style_conditional.data_range
#end if
file_type = bigwig
+#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 != "":
[spacer]
-#if $track.track_file_style_conditional.spacer_height:
height = $track.track_file_style_conditional.spacer_height
#end if
#end for
@@ -307,8 +382,11 @@
#end if
file_type = bedgraph_matrix
plot horizontal lines=False
+#if $track.track_file_style_conditional.invert_orientation:
+orientation = inverted
+#end if
+#if $track.track_file_style_conditional.spacer_height != "":
[spacer]
-#if $track.track_file_style_conditional.spacer_height:
height = $track.track_file_style_conditional.spacer_height
#end if
#end for
@@ -323,8 +401,8 @@
#end if
#if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
+#if $track.track_file_style_conditional.spacer_height != "":
[spacer]
-#if $track.track_file_style_conditional.spacer_height:
height = $track.track_file_style_conditional.spacer_height
#end if
#end if
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