--- a/macros_conffiles.xml	Thu Jan 23 07:27:22 2020 -0500
+++ b/macros_conffiles.xml	Fri May 01 07:28:50 2020 -0400
@@ -7,6 +7,11 @@
 <<include colors_fonts_patterns.conf>>
 <<include housekeeping.conf>>
 
+max_ticks*            = ${limits.max_ticks}
+max_ideograms*        = ${limits.max_ideograms}
+max_links*            = ${limits.max_links}
+max_points_per_track* = ${limits.max_points_per_track}
+
 <colors>
 <<include karyotype-colors.conf>>
 
@@ -50,7 +55,8 @@
   svg                = yes
 #end if
   # by default angle = 0 is at 3 o'clock position
-  angle_offset       = -90
+  angle_offset       = ${ideogram.angle_offset}
+  angle_orientation  = ${ideogram.angle_orientation}
   auto_alpha_colors  = yes
   auto_alpha_steps   = 5
 #if str($plot_options.background.background_select) == 'transparent':
@@ -61,10 +67,20 @@
   radius*            = ${plot_options.radius}p
 </image>
 
+<zooms>
+  #for zoom in $scaling.zooms:
+    <zoom>
+        chr   = ${zoom.chr}
+        start = ${zoom.start}u
+        end   = ${zoom.end}u
+        scale = ${zoom.scale}
+    </zoom>
+  #end for
+</zooms>
+
 <<include ticks.conf>>
 <<include ideogram.conf>>
 <<include data.conf>>
-<<include highlight.conf>>
 <<include links.conf>>
 
     ]]></configfile>
@@ -73,7 +89,7 @@
     <configfile name="ticks_conf"><![CDATA[
 @UTILS@
 
-show_ticks          = ${ticks.show_ticks}
+show_ticks          = yes
 show_tick_labels    = yes
 
 
@@ -97,7 +113,7 @@
 
     #for $tick_group in $ticks.tick_group:
     <tick>
-        spacing        = ${tick_group.spacing}
+        spacing        = ${tick_group.spacing}u
         size           = ${tick_group.size}p
         show_label     = ${tick_group.ticks.show_tick_labels}
         color          = $circosColor($tick_group.color)
@@ -131,7 +147,13 @@
 <ideogram>
     <spacing>
         ## spacing between ideograms
-        default = ${ideogram.spacing}r
+        default = ${ideogram.spacing}u
+
+        #for pairwise in $ideogram.pairwise_spacing
+        <pairwise ${pairwise.chr1} ${pairwise.chr2}>
+            spacing = ${pairwise.spacing}u
+        </pairwise>
+        #end for
     </spacing>
 
     # ideogram position, thickness and fill
@@ -143,7 +165,7 @@
     label_size       = ${ideogram.ideogram_labels.size}
     label_parallel   = ${ideogram.ideogram_labels.parallel}
 
-  #if $ideogram.bands.bands:
+  #if $ideogram.bands.show_bands:
     show_bands            = yes
   #else
     show_bands            = no
@@ -157,77 +179,6 @@
 </ideogram>
 ]]></configfile>
   </xml>
-  <xml name="configfile_highlight_conf">
-    <configfile name="highlight_conf"><![CDATA[
-@UTILS@
-<highlights>
-#for $hi, $data in enumerate($sec_highlight.data):
-    <highlight>
-    file             = data/highlight-${hi}.txt # ${data.data_source.element_identifier}
-    r1               = ${data.r1}r
-    r0               = ${data.r0}r
-    fill_color       = $circosColorAlpha($data.fill_color, $data.fill_color_alpha)
-    stroke_color     = $circosColorAlpha($data.stroke_color, $data.stroke_color_alpha)
-    stroke_thickness = ${data.stroke_thickness}
-
-    <rules>
-    #for $rule in $data.sec_rule.rules:
-        <rule>
-            #for $condition in $rule.conditions
-                #if str($condition.application.application_select) == "1":
-                    condition = 1
-                #elif str($condition.application.application_select) == "on":
-                    condition = on($condition.application.on_genomes)
-                #elif str($condition.application.application_select) == "pos":
-                    #if $condition.application.pos_gt:
-                    condition = var(start) > $condition.application.pos_gt
-                    #end if
-
-                    #if $condition.application.pos_lt:
-                        #if $condition.application.pos_lt_sub == 'yes':
-                    condition = var(end) < chrlen(var(chr)) - $condition.application.pos_lt
-                        #else
-                    condition = var(end) < $condition.application.pos_lt
-                        #end if
-                    #end if
-                #elif str($condition.application.application_select) == "value":
-                    #if $condition.application.pos_gt:
-                    condition = var(value) > $condition.application.pos_gt
-                    #end if
-
-                    #if $condition.application.pos_lt:
-                    condition = var(value) < $condition.application.pos_lt
-                    #end if
-                #elif str($condition.application.application_select) == "var":
-                    condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
-                #elif str($condition.application.application_select) == "random":
-                    condition = rand() < ${condition.application.value}
-                #end if
-            #end for
-
-            #for $action in $rule.actions:
-                #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
-                    #set x_fill_color = $action.action.action_value
-                    #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
-                    #set x_min = $x_fill_color_count if $action.action.invert else 1
-                    #set x_max = 1 if $action.action.invert else $x_fill_color_count
-                    #set color_action = "fill_color" if str($plot_type) in ('histogram', 'histogram-stacked') else "color"
-
-                    $color_action = eval(sprintf("${action.action.action_value}-%d", remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, ${x_min}, ${x_max})))
-                #else
-                    $action.action.action_select = $circosColor($action.action.action_value)
-                #end if
-            #end for
-            $rule.continue_flow
-        </rule>
-    #end for
-    </rules>
-    </highlight>
-#end for
-</highlights>
- ]]></configfile>
-  </xml>
-
 
   <xml name="configfile_data_conf">
     <configfile name="data_conf"><![CDATA[
@@ -240,11 +191,15 @@
     file        = data/data-${hi}.txt # ${data.plot_format.data_source.element_identifier}
     r1          = ${data.r1}r
     r0          = ${data.r0}r
+    #if str($data.zdepth) != '':
+    z           = ${data.zdepth}
+    #end if
     orientation = ${data.orientation}
     #if str($data.minmax.minmax_select) == 'yes':
     min         = ${$data.minmax.min_value}
     max         = ${$data.minmax.max_value}
     #end if
+    minsize     = ${data.minsize}u
 
 #if str($plot_type) in ('histogram', 'histogram-stacked'):
     type       = histogram
@@ -257,14 +212,27 @@
     fill_under = ${data.plot_format.format_specific.fill_under}
     color      = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
     thickness  = ${data.plot_format.format_specific.stroke_thickness}
+#else if str($plot_type) == 'highlight':
+    type       = ${plot_type}
+    fill_color = $circosColorAlpha($data.plot_format.format_specific.fill_color, $data.plot_format.format_specific.fill_color_alpha)
+    color      = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
+    thickness  = ${data.plot_format.format_specific.stroke_thickness}
 #else if str($plot_type) == 'heatmap':
     type       = ${plot_type}
-    color      = ${data.plot_format.format_specific.fill_color}
+    color      = ${data.plot_format.format_specific.color_scale.fill_color}
+    color_mapping = ${data.plot_format.format_specific.color_mapping}  # http://www.circos.ca/documentation/tutorials/2d_tracks/heat_maps/
     scale_log_base = ${data.plot_format.format_specific.scale_log_base}
+    stroke_color     = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
+    stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
 #else if str($plot_type) == 'line':
     type       = ${plot_type}
-    color      = $circosColor($data.plot_format.format_specific.stroke_color)
+    color      = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
     thickness  = ${data.plot_format.format_specific.stroke_thickness}
+#else if str($plot_type) == 'connector':
+    type       = ${plot_type}
+    color      = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
+    thickness  = ${data.plot_format.format_specific.stroke_thickness}
+    connector_dims = ${data.plot_format.format_specific.connector_dims}
 #else if str($plot_type) == 'scatter':
     type             = ${plot_type}
     glyph            = ${data.plot_format.format_specific.glyph}
@@ -276,13 +244,13 @@
     #
     # Additionally it is named "color" in a scatter track whilst in the rule
     # you must override it with "fill_color"
-    color            = $circosColor($data.plot_format.format_specific.fill_color)
-    stroke_color     = $circosColor($data.plot_format.format_specific.stroke_color)
+    color            = $circosColorAlpha($data.plot_format.format_specific.fill_color, $data.plot_format.format_specific.fill_color_alpha)
+    stroke_color     = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
     stroke_thickness = ${data.plot_format.format_specific.stroke_thickness}
 #else if str($plot_type) == 'tile':
     type                  = ${plot_type}
     color                 = color-tile-$hi
-    stroke_color          = $circosColor($data.plot_format.format_specific.stroke_color)
+    stroke_color          = $circosColorAlpha($data.plot_format.format_specific.stroke_color, $data.plot_format.format_specific.stroke_color_alpha)
     stroke_thickness      = ${data.plot_format.format_specific.stroke_thickness}
     layers                = ${data.plot_format.format_specific.layers}
     thickness             = ${data.plot_format.format_specific.thickness}
@@ -324,36 +292,41 @@
         <rule>
             # Workaround for above commented colour bug.
             condition  = 1
-            fill_color = $circosColor($data.plot_format.format_specific.fill_color)
+            fill_color = $circosColorAlpha($data.plot_format.format_specific.fill_color, $data.plot_format.format_specific.fill_color_alpha)
             flow       = continue
         </rule>
     #end if
     #for $rule in $data.sec_rule.rules:
         <rule>
             #for $condition in $rule.conditions
-                #if str($condition.application.application_select) == "1":
+                #set cond = $condition.application.application_select
+                #if $cond == "always":
                     condition = 1
-                #elif str($condition.application.application_select) == "on":
+                #elif $cond == 'random'
+                    condition = rand() < ${condition.application.value}
+                #elif $cond == "on":
                     #set on_str = ' '.join([ "on(%s)" % $chr.strip() for $chr in $condition.application.on_genomes.split(',') ])
                     condition = $on_str
-                #elif str($condition.application.application_select) == "pos":
-                    #if $condition.application.pos_gt:
+                #elif $cond == "pos":
+                    #if str($condition.application.pos_gt) != '':
                     condition = var(start) > $condition.application.pos_gt
                     #end if
 
-                    #if $condition.application.pos_lt:
+                    #if str($condition.application.pos_lt) != '':
                     condition = var(start) < $condition.application.pos_lt
                     #end if
-                #elif str($condition.application.application_select) == "value":
-                    #if $condition.application.pos_gt:
+                #elif $cond == "value":
+                    #if str($condition.application.pos_gt) != '':
                     condition = var(value) > $condition.application.pos_gt
                     #end if
 
-                    #if $condition.application.pos_lt:
+                    #if str($condition.application.pos_lt) != '':
                     condition = var(value) < $condition.application.pos_lt
                     #end if
-                #elif str($condition.application.application_select) == "var":
+                #elif $cond == "var":
                     condition = var(${condition.application.varname}) ${condition.application.cond_select} "${condition.application.varvalue}"
+                #else
+                    condition = 0 # Error: the Galaxy devs forgot a case
                 #end if
             #end for
 
@@ -386,22 +359,39 @@
     </rules>
 
     <axes>
+        #if str($data.sec_axes.only_if_data) == "data":
+        show  = data
+        #end if
         #for $axis in $data.sec_axes.axes:
         <axis>
-            color     = $circosColor($axis.color)
+            color     = $circosColorAlpha($axis.color, $axis.color_alpha)
             thickness = ${axis.thickness}
-            spacing   = ${axis.spacing}r
+            #if str($axis.radial_position.select) == 'plot':
+            spacing   = ${axis.radial_position.spacing}r
             y0        = ${axis.y0}r
             y1        = ${axis.y1}r
+            #else:
+            spacing   = ${axis.radial_position.spacing}
+            y0        = ${axis.y0}
+            y1        = ${axis.y1}
+            #end if
         </axis>
         #end for
     </axes>
     <backgrounds>
+        #if str($data.sec_bkgs.only_if_data) == "data":
+        show  = data
+        #end if
         #for $bkg in $data.sec_bkgs.backgrounds:
         <background>
-            color = $circosColor($bkg.color)
-            y0    = ${bkg.y0}r
-            y1    = ${bkg.y1}r
+            color = $circosColorAlpha($bkg.color, $bkg.color_alpha)
+            #if str($bkg.radial_position.select) == 'plot':
+            y0    = ${bkg.radial_position.y0}r
+            y1    = ${bkg.radial_position.y1}r
+            #else:
+            y0    = ${bkg.radial_position.y0}
+            y1    = ${bkg.radial_position.y1}
+            #end if
         </background>
         #end for
     </backgrounds>
@@ -419,7 +409,9 @@
 <link>
     file                 = data/links-${hi}.txt # ${data.data_source.element_identifier}
     radius               = ${data.radius}r
+    z                    = ${data.zdepth}
     ribbon               = ${data.linktype.ribbon}
+    minsize              = ${data.minsize}u
   #if $data.linktype.ribbon == 'yes'
     ${data.linktype.twist}
    #if $data.linktype.pattern != 'solid':
@@ -437,34 +429,30 @@
     perturb_bezier_radius        = ${data.advanced.perturbation.perturb_bezier_radius_min},${data.advanced.perturbation.perturb_bezier_radius_max}
     perturb_bezier_radius_purity = ${data.advanced.perturbation.perturb_bezier_radius_purity_min},${data.advanced.perturbation.perturb_bezier_radius_purity_max}
   #end if
-  #if $data.advanced.zdepth
-    z                    = ${data.advanced.zdepth}
-  #end if
 
     <rules>
     #for $rule in $data.sec_link_rule.rules:
         <rule>
             #for $condition in $rule.conditions
                 #set cond = $condition.application.application_select
-                #if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev'
-                    condition = var($cond)
-                #elif $cond == 'always'
+                #if $cond == 'always'
                     condition = 1
                 #elif $cond == 'random'
                     condition = rand() < ${condition.application.value}
+                #elif $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev'
+                    condition = var($cond)
                 #else
                     #set op = $condition.application.comparison.compare
                     #set val = $condition.application.comparison.compval
                     #if $cond == 'chr'
                         #if $op == 'between' or $op == 'fromto'
                             #set val2 = $condition.application.comparison.compval2
-                            #set c=''.join([str($op),"(",str($val),",",str($val2),")"])
+                            condition = ${op}(${val}, ${val2})
                         #elif $op == 'on'
-                            #set c='(var(chr1) eq "%s" or var(chr2) eq "%s")' % (str($val), str($val))
+                            condition = var(chr1) eq "${val}" or var(chr2) eq "${val}"
                         #else
-                            #set c=''.join([str($op),"(",str($val),")"])
+                            condition = ${op}(${val})
                         #end if
-                        condition = $c
                     #else
                         #if $cond == 'dist' and $op == 'lt'
                             condition = abs(var(pos1) - var(pos2)) < $val
@@ -481,30 +469,27 @@
 
             #for $action in $rule.actions:
                 #set actiontype = $action.action.action_select
-                #if $actiontype == 'color':
+                #if $actiontype in ('color', 'stroke_color'):
                     #if $action.action.dynamic.dynamic_select == "static":
                         #set actionval = $circosColorAlpha($action.action.dynamic.action_value, $action.action.dynamic.action_value_alpha)
                         $actiontype = $actionval
-                    #else
-                        #set x_fill_color = $action.action.dynamic.action_value
-                        #set x_fill_color_count = int(str($x_fill_color).split('-')[1])
-                        #set x_min = $x_fill_color_count if $action.action.dynamic.invert else 1
-                        #set x_max = 1 if $action.action.dynamic.invert else $x_fill_color_count
-
-                        $actiontype = eval(sprintf("${action.action.dynamic.action_value}-%d", remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max})))
+                    #elif $action.action.dynamic.dynamic_select == 'source':
+                        $actiontype = eval(var(chr1))
+                    #elif $action.action.dynamic.dynamic_select == 'dest':
+                        $actiontype = eval(var(chr2))
                     #end if
                 #elif $actiontype == 'z':
                     #if $action.action.dynamic.dynamic_select == "static":
-                        #set actionval = $action.action.dynamic.action_value
-                        $actiontype = $actionval
+                        $actiontype = ${action.action.dynamic.action_value}
                     #else
                         #set x_min = 1000 if $action.action.dynamic.invert else 1
                         #set x_max = 1 if $action.action.dynamic.invert else 1000
                         $actiontype = eval(remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, ${x_min}, ${x_max}))
                     #end if
+                #elif $actiontype == 'value_from_attr':
+                    value = var(${action.action.action_value})
                 #else
-                    #set actionval = $action.action.action_value
-                    $actiontype = $actionval
+                    $actiontype = ${action.action.action_value}
                 #end if
             #end for