# HG changeset patch # User iuc # Date 1759347307 0 # Node ID 86d0ebe0962899ea1a355406c51e5f635b59875c # Parent 36b848d5f3ec21d886e4577569be2667fa6e7d94 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 9fdf4ad9c2a9c026720e2b01460b7ac85056b068 diff -r 36b848d5f3ec -r 86d0ebe09628 macros.xml --- a/macros.xml Tue Mar 12 10:28:03 2024 +0000 +++ b/macros.xml Wed Oct 01 19:35:07 2025 +0000 @@ -1,6 +1,6 @@ - 3.8 - 2 + 3.9 + 0 pygenometracks @@ -13,7 +13,6 @@ pygenometracks - 10.1038/s41467-017-02525-w @@ -45,9 +44,6 @@ - - - @@ -212,24 +208,11 @@ -
- - - - - - - - - - - -
- + + + @@ -243,6 +226,116 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+ + +
+ + + + +
+
+ +
+ + + + + +
+
+ + +
+ + + + + +
+
+
+
+ + + + + + + + + + + + + + + + + diff -r 36b848d5f3ec -r 86d0ebe09628 pyGenomeTracks.xml --- a/pyGenomeTracks.xml Tue Mar 12 10:28:03 2024 +0000 +++ b/pyGenomeTracks.xml Wed Oct 01 19:35:07 2025 +0000 @@ -219,15 +219,17 @@ ## 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): + #for $counter_bed, $data_bed in enumerate($track.track_file_style_conditional.bed_gtf.track_input_bed): [genes_${counter}_${counter_bed}] - #set ext = $data_bed.extension file = $data_bed - #if $ext == 'gtf': -prefered_name = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.prefered_name - #if $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_transcripts_select == 'true': + #if $track.track_file_style_conditional.bed_gtf.input_bed_or_gtf == "bed": +file_type = bed + #else: +file_type = gtf +prefered_name = $track.track_file_style_conditional.bed_gtf.prefered_name + #if $track.track_file_style_conditional.bed_gtf.merge_transcripts.merge_transcripts_select == 'true': merge_transcripts = true -merge_overlapping_exons = $track.track_file_style_conditional.bed_style.bed_advanced.gtf.merge_transcripts.merge_overlapping_exons +merge_overlapping_exons = $track.track_file_style_conditional.bed_gtf.merge_transcripts.merge_overlapping_exons #end if #end if #if $track.track_file_style_conditional.title: @@ -248,66 +250,109 @@ #end if #end if #end if - #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 -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 - #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': -color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color - #else -color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select +display = $track.track_file_style_conditional.display_cond.display + #if $track.track_file_style_conditional.display_cond.display in ['stacked', 'interleaved', 'collapsed']: +style = $track.track_file_style_conditional.display_cond.bed_style.bed_style_select + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows', 'flybase']: + #if $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.border_color_bed_select == 'manually': +border_color = $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.color + #else +border_color = $track.track_file_style_conditional.display_cond.bed_style.border_color_bed.border_color_bed_select + #end if #end if - #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 + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows']: +arrow_interval = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_interval + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color_arrow_select == "manually": +color_arrow = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color + #else +color_arrow = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_arrow.color_arrow_select + #end if + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'UCSC': + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': +color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.color + #else +color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select + #end if #else: - ## This is 'like' - #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb": + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color_utr_select == 'manually': +color_utr = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color + #elif $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.color_utr.color_utr_select == 'bed_rgb': color_utr = bed_rgb #else: + ## This is 'like' + #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.display_cond.bed_style.bed_style_select in ['flybase', 'tssarrow']: +height_utr = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.height_utr + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'exonarrows': +height_intron = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.height_intron + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'tssarrow' and $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_length != '': +arrow_length = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrow_length + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select == 'flybase': +arrowhead_included = $track.track_file_style_conditional.display_cond.bed_style.arrowhead_included +arrowhead_fraction = $track.track_file_style_conditional.display_cond.bed_style.arrowhead_fraction + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': +color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.color + #else +color_backbone = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select + #end if #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 + #if $track.track_file_style_conditional.display_cond.bed_style.bed_style_select in ['UCSC', 'exonarrows', 'tssarrow']: +arrowhead_fraction = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.arrowhead_fraction + #end if + #if $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.gene_rows: +gene_rows = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.gene_rows #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 -arrowhead_fraction = $track.track_file_style_conditional.bed_style.arrowhead_fraction - #if $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select == 'manually': -color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.color - #else -color_backbone = $track.track_file_style_conditional.bed_style.bed_advanced.backbone_color_bed.backbone_color_bed_select +global_max_row = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.global_max_row +max_labels = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.max_labels +line_width = $track.track_file_style_conditional.display_cond.bed_style.bed_advanced.line_width +labels = $track.track_file_style_conditional.display_cond.labels.plot_labels + #if $track.track_file_style_conditional.display_cond.labels.plot_labels == 'true': +all_labels_inside = $track.track_file_style_conditional.display_cond.labels.all_labels_inside +labels_in_margin = $track.track_file_style_conditional.display_cond.labels.labels_in_margin +fontstyle = $track.track_file_style_conditional.display_cond.labels.fontstyle + #if $track.track_file_style_conditional.display_cond.labels.fontsize: +fontsize = $track.track_file_style_conditional.display_cond.labels.fontsize #end if #end if #end if -display = $track.track_file_style_conditional.display + #if $track.track_file_style_conditional.display_cond.display in ['triangle', 'squares']: + #if $track.track_file_style_conditional.display_cond.border_color_bed.border_color_bed_select == 'manually': +border_color = $track.track_file_style_conditional.display_cond.border_color_bed.color + #else +border_color = $track.track_file_style_conditional.display_cond.border_color_bed.border_color_bed_select + #end if + #end if + #if $track.track_file_style_conditional.display_cond.display in ['inversions', 'deletions', 'triangles', 'squares']: +line_width = $track.track_file_style_conditional.display_cond.line_width + #end if + #if $track.track_file_style_conditional.display_cond.display in ['inversions', 'deletions']: +labels = $track.track_file_style_conditional.display_cond.labels.plot_labels + #if $track.track_file_style_conditional.display_cond.labels.plot_labels == 'true': +fontstyle = $track.track_file_style_conditional.display_cond.labels.fontstyle + #if $track.track_file_style_conditional.display_cond.labels.fontsize: +fontsize = $track.track_file_style_conditional.display_cond.labels.fontsize + #end if + #end if + #end if + #if $track.track_file_style_conditional.display_cond.display == 'deletions': +backbone_color = $track.track_file_style_conditional.display_cond.backbone_color + #end if + #if $track.track_file_style_conditional.display_cond.display == 'inversions': +arrowhead_fraction = $track.track_file_style_conditional.display_cond.arrowhead_fraction + #end if #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.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 -fontstyle = $track.track_file_style_conditional.labels.fontstyle - #if $track.track_file_style_conditional.labels.fontsize: -fontsize = $track.track_file_style_conditional.labels.fontsize - #end if - #end if -file_type = $ext - #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_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 @@ -770,6 +815,7 @@ species_order_only = $track.track_file_style_conditional.species_order_only #end if display_ref_seq = $track.track_file_style_conditional.display_ref_seq +rasterize = $track.track_file_style_conditional.rasterize file_type = maf ## If spacer is asked a new section is created: #if $track.track_file_style_conditional.spacer_height != "": @@ -921,8 +967,32 @@ - - + + + + + + + + + + + + + + + + + + + + + + + + @@ -942,74 +1012,49 @@ - - - - - + + + + + + + + + - - - - - - - - - + + + + + - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + -
- - - -
-
- -
- - - -
-
- -
- - - -
+ label="Parameter to control the size of the arrows"/> + +
- @@ -1314,6 +1359,8 @@ label="Display only the species specified above"/> + @@ -1461,11 +1508,16 @@ - + + + + - - + + + + @@ -1478,16 +1530,21 @@ - + + + + - - - - -
- -
+ + + + + +
+ +
+
@@ -1500,16 +1557,21 @@ - + + + + - - - - -
- -
+ + + + + +
+ +
+
@@ -1520,7 +1582,7 @@
- + @@ -1596,7 +1658,7 @@ - + @@ -1741,30 +1803,40 @@ - + + + + - - - - - + + + + + + + - + + + + - - - - -
- -
+ + + + + +
+ +
+
@@ -1777,60 +1849,81 @@ - + + + + - - - + + + + + + + + + + + - - - - - + + + + - - + + + + + + + + + + - - - - - + + + + - - + + + + + + + + + + - - - - - +
@@ -1839,7 +1932,7 @@ - +
@@ -1854,8 +1947,8 @@ -
+
@@ -1868,7 +1961,7 @@ - + @@ -1882,12 +1975,19 @@ - + + + + - - - + + + + + + + @@ -1895,18 +1995,25 @@ - + + + + - - - + + + + + + + - + @@ -1979,7 +2086,7 @@ - + @@ -1993,7 +2100,10 @@ - + + + + @@ -2001,55 +2111,64 @@ - + + + + + + + + + - -
- - - - - -
- - - - + + +
+ + + +
-
+ - + + + + + + + + + - -
- - - - - -
- - - - + + +
+ + + +
-
- + + - + + + + @@ -2061,57 +2180,72 @@ - + + + + - -
- - - -
+ + +
+ + + +
+
- + + + + - - - + + + + + - + + + + - -
- - - -
-
- - - + + +
+ + + +
+
+ + + +
- + @@ -2125,35 +2259,72 @@ - - + + + + + - - -
- - -
+ + + +
+ + +
+
- - + + + + + - - -
- - -
+ + + +
+ + + + + +
+
+
+
+
+ + + + + + + + + + + + +
+ + + + + + +
+
- +
@@ -2167,42 +2338,57 @@ - + + + + - - + + + + - + + + + - - - - - + + + + + + + - + + + + - - + + + + @@ -2210,7 +2396,10 @@ - + + + + @@ -2218,8 +2407,10 @@ - - + + + + @@ -2243,7 +2434,7 @@ - + @@ -2257,13 +2448,19 @@ - + + + + - + + + + @@ -2293,7 +2490,7 @@
- + @@ -2352,7 +2549,7 @@ - + @@ -2404,7 +2601,7 @@ - + @@ -2463,7 +2660,7 @@ - + @@ -2503,7 +2700,7 @@ - + @@ -2517,69 +2714,124 @@ - + + + + - - -
- - + + + +
+ + + + +
+
+
+
+ + + + + + + + + + + + + +
+ + + - -
+
+
+
- - + + + + + - - -
- - - - - -
+ + + + + +
+
+ + + + + + + + + + + + +
+ + +
+
- - - - - + + + + + + + + - - - - - - - - - -
- -
+ + + + + + + +
+ + + + + + + + +
+
- +
- +
@@ -2587,7 +2839,7 @@ - +
@@ -2602,8 +2854,8 @@ -
+
@@ -2616,7 +2868,7 @@ - + @@ -2739,7 +2991,7 @@ - + @@ -2817,7 +3069,7 @@ - + @@ -2948,7 +3200,7 @@ - + @@ -2969,7 +3221,7 @@ - + @@ -3013,7 +3265,7 @@ - + @@ -3058,7 +3310,7 @@ - + @@ -3136,7 +3388,7 @@ - + @@ -3173,7 +3425,7 @@ - + @@ -3267,7 +3519,7 @@ - + @@ -3314,7 +3566,6 @@ - @@ -3324,7 +3575,7 @@ - + @@ -3353,7 +3604,117 @@ - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +