Mercurial > repos > iuc > circos

diff macros_conffiles.xml @ 2:014a21767ac4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 076837a2e9c2b6ececcea4aa286ea7a412387a96"
author iuc
date Tue, 17 Sep 2019 16:54:57 -0400
parents ef5f8bbf7730
children 184dfd9e113d
line wrap: on
line diff
--- a/macros_conffiles.xml	Thu Oct 04 06:05:31 2018 -0400
+++ b/macros_conffiles.xml	Tue Sep 17 16:54:57 2019 -0400
@@ -2,55 +2,123 @@
 <macros>
   <xml name="configfile_circos_conf">
     <configfile name="circos_conf"><![CDATA[
+@UTILS@
+
 <<include colors_fonts_patterns.conf>>
 <<include housekeeping.conf>>
+
+<colors>
+<<include karyotype-colors.conf>>
+
+#for $hi, $data in enumerate($sec_tdd.data):
+    #set plot_type = str($data.plot_format.plot_format_select)
+    #if str($plot_type) == 'tile':
+        color-tile-$hi = $circosColor($data.plot_format.format_specific.fill_color)
+    #end if
+#end for
+</colors>
+
 karyotype = karyotype.txt
+#if str($ideogram.units) == 'bases':
+chromosomes_units = 1
+#else if str($ideogram.units) == 'kb':
+chromosomes_units = 1000
+#else if str($ideogram.units) == 'mb':
+chromosomes_units = 1000000
+#else:
+chromosomes_units = 1000000000
+#end if
+
+#if $ideogram.limit_chromosomes:
+chromosomes = $ideogram.limit_chromosomes
+chromosomes_order = $chromosomesToOrder($ideogram.limit_chromosomes)
+chromosomes_display_default = no
+#end if
+
+#if $ideogram.chromosomes_reverse:
+chromosomes_reverse = $ideogram.chromosomes_reverse
+#end if
 
 <image>
-  <<include etc/image.conf>>
+  # Transcluded from etc/image.generic.conf
+  dir                = .
+  file               = circos.png
+#if $outputs.png:
+  png                = yes
+#end if
+#if $outputs.svg:
+  svg                = yes
+#end if
+  # by default angle = 0 is at 3 o'clock position
+  angle_offset       = -90
+  auto_alpha_colors  = yes
+  auto_alpha_steps   = 5
+#if str($plot_options.background.background_select) == 'transparent':
+  background         = transparent
+#else
+  background         = $circosColor($plot_options.background.background_color)
+#end if
+  radius*            = ${plot_options.radius}p
 </image>
 
 <<include ticks.conf>>
 <<include ideogram.conf>>
-<plots>
-    <<include 2d.conf>>
-</plots>
-<links>
-    <<include links.conf>>
-</links>
+<<include data.conf>>
+<<include highlight.conf>>
+<<include links.conf>>
 
     ]]></configfile>
   </xml>
   <xml name="configfile_ticks_conf">
     <configfile name="ticks_conf"><![CDATA[
+@UTILS@
+
 show_ticks          = ${ticks.show_ticks}
 show_tick_labels    = yes
 
-#def circosColor($value)
-    #set $value = str($value)
-    #set $r = int($value[1:3], 16)
-    #set $g = int($value[3:5], 16)
-    #set $b = int($value[5:], 16)
-    $r, $g, $b
-#end def
-
 
 <ticks>
     radius           = ${ticks.radius}r
-    color            = $circosColor($ticks.color)
+    color            = black
+    skip_first_label = ${ticks.skip_first_label}
+    skip_last_label  = ${ticks.skip_last_label}
     thickness        = 2p
-    multiplier       = ${ticks.multiplier}
+
+    # Multiplier controls how 'u' behaves when used in numbers.
+    #if str($ideogram.units) == 'bases':
+    multiplier       = 1
+    #else if str($ideogram.units) == 'kb':
+    multiplier       = 1e-3
+    #else if str($ideogram.units) == 'mb':
+    multiplier       = 1e-6
+    #else if str($ideogram.units) == 'gb':
+    multiplier       = 1e-9
+    #end if
 
     #for $tick_group in $ticks.tick_group:
     <tick>
         spacing        = ${tick_group.spacing}
         size           = ${tick_group.size}p
-        show_label     = ${tick_group.show_tick_labels}
-        label_size     = ${tick_group.label_size}p
-        label_offset   = ${tick_group.label_offset}p
-        format         = ${tick_group.format} kb
-        ## TODO: figure out automated tick labels
-        ##if ${ticks.multiplier} * ${tick_group.spacing}
+        show_label     = ${tick_group.ticks.show_tick_labels}
+        color          = $circosColor($tick_group.color)
+
+      #if str($tick_group.ticks.show_tick_labels) == 'yes':
+        label_size     = ${tick_group.ticks.label_size}p
+        label_offset   = ${tick_group.ticks.label_offset}p
+      #if $tick_group.ticks.format_ext:
+       #if str($ideogram.units) == 'bases':
+        format         = ${tick_group.ticks.format}
+       #else if str($ideogram.units) == 'kb':
+        format         = ${tick_group.ticks.format} Kb
+       #else if str($ideogram.units) == 'mb':
+        format         = ${tick_group.ticks.format} Mb
+       #else if str($ideogram.units) == 'gb':
+        format         = ${tick_group.ticks.format} Gb
+       #end if
+      #else
+        format = ${tick_group.ticks.format}
+    #end if
+      #end if
     </tick>
     #end for
 </ticks>
@@ -59,9 +127,8 @@
   </xml>
   <xml name="configfile_ideogram_conf">
     <configfile name="ideogram_conf"><![CDATA[
-
+@UTILS@
 <ideogram>
-
     <spacing>
         ## spacing between ideograms
         default = ${ideogram.spacing}r
@@ -71,67 +138,35 @@
     radius           = ${ideogram.radius}r
     thickness        = ${ideogram.thickness}p
     fill             = yes
-
     show_label       = ${ideogram.ideogram_labels.show_label}
-    label_radius     = dims(ideogram,radius) + 0.075r
-    label_size       = 24
+    label_radius     = dims(ideogram,radius) + ${ideogram.ideogram_labels.radius_offset}r
+    label_size       = ${ideogram.ideogram_labels.size}
     label_parallel   = ${ideogram.ideogram_labels.parallel}
 
+  #if $ideogram.bands.bands:
     show_bands            = yes
-    fill_bands            = yes
-    band_transparency     = 4
-
+  #else
+    show_bands            = no
+  #end if
+    fill_bands            = ${ideogram.bands.fill_bands}
+  #if int($ideogram.bands.band_transparency) > 0:
+    band_transparency     = ${ideogram.bands.band_transparency}
+  #end if
+    band_stroke_color     = $circosColor($ideogram.bands.band_stroke_color)
+    band_stroke_thickness = ${ideogram.bands.band_stroke_thickness}
 </ideogram>
 ]]></configfile>
   </xml>
-  <xml name="configfile_data_conf">
-    <configfile name="data_conf"><![CDATA[
-#for $hi, $data in enumerate($sec_tdd.data):
-<plot>
-    #set plot_type = str($data.plot_format.plot_format_select)
-    #def circosColor($value)
-        #set $value = str($value)
-        #set $r = int($value[1:3], 16)
-        #set $g = int($value[3:5], 16)
-        #set $b = int($value[5:], 16)
-        $r, $g, $b
-    #end def
-
-    type = ${plot_type}
-    file = data/data-${hi}.txt
-
-    r1   = ${data.r1}r
-    r0   = ${data.r0}r
-    orientation = ${data.orientation}
-
-#if str($plot_type) == 'histogram':
-    extend_bin = ${data.plot_format.format_specific.extend_bins}
-    fill_color = ${data.plot_format.format_specific.fill_color}
-#else if str($plot_type) == 'heatmap':
-    color = $circosColor($data.plot_format.format_specific.fill_color)
-    scale_log_base = ${data.plot_format.format_specific.scale_log_base}
-#else if str($plot_type) == 'line':
-    color     = $circosColor($data.plot_format.format_specific.color)
-    thickness = ${data.plot_format.format_specific.thickness}
-#else if str($plot_type) == 'scatter':
-    glyph                = ${data.plot_format.format_specific.glyph}
-    glyph_size           = ${data.plot_format.format_specific.glyph_size}
-    color                = $circosColor($data.plot_format.format_specific.color)
-    stroke_color         = $circosColor($data.plot_format.format_specific.stroke_color)
-    stroke_thickness     = ${data.plot_format.format_specific.stroke_thickness}
-#else if str($plot_type) == 'tile':
-    color                = ${data.plot_format.format_specific.color}
-    stroke_color         = $circosColor($data.plot_format.format_specific.color)
-    stroke_thickness     = ${data.plot_format.format_specific.stroke_thickness}
-    layers               = ${data.plot_format.format_specific.layers}
-    thickness            = ${data.plot_format.format_specific.thickness}
-    padding              = ${data.plot_format.format_specific.padding}
-
-    layers_overflow       = ${data.plot_format.format_specific.overflow.overflow_behavior}
-    #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
-    layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
-    #end if
-#end if
+  <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 = $circosColor($data.fill_color)
 
     <rules>
     #for $rule in $data.sec_rule.rules:
@@ -143,19 +178,177 @@
                     #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 float($condition.application.pos_gt) != 0:
+                    #if $condition.application.pos_gt:
                     condition = var(start) > $condition.application.pos_gt
                     #end if
 
-                    #if float($condition.application.pos_lt) != 0:
+                    #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[
+<plots>
+@UTILS@
+
+#for $hi, $data in enumerate($sec_tdd.data):
+<plot>
+    #set plot_type = str($data.plot_format.plot_format_select)
+    file        = data/data-${hi}.txt # ${data.plot_format.data_source.element_identifier}
+    r1          = ${data.r1}r
+    r0          = ${data.r0}r
+    orientation = ${data.orientation}
+    #if str($data.minmax.minmax_select) == 'yes':
+    min         = ${$data.minmax.min_value}
+    max         = ${$data.minmax.max_value}
+    #end if
+
+#if str($plot_type) in ('histogram', 'histogram-stacked'):
+    type       = histogram
+    extend_bin = ${data.plot_format.format_specific.extend_bins}
+    #if str($plot_type) == 'histogram':
+    fill_color = $circosColorAlpha($data.plot_format.format_specific.fill_color, $data.plot_format.format_specific.fill_color_alpha)
+    #else:
+    fill_color = $data.plot_format.format_specific.fill_color
+    #end if
+    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) == 'heatmap':
+    type       = ${plot_type}
+    color      = ${data.plot_format.format_specific.fill_color}
+    scale_log_base = ${data.plot_format.format_specific.scale_log_base}
+#else if str($plot_type) == 'line':
+    type       = ${plot_type}
+    color      = $circosColor($data.plot_format.format_specific.stroke_color)
+    thickness  = ${data.plot_format.format_specific.stroke_thickness}
+#else if str($plot_type) == 'scatter':
+    type             = ${plot_type}
+    glyph            = ${data.plot_format.format_specific.glyph}
+    glyph_size       = ${data.plot_format.format_specific.glyph_size}
+    # So this option is ignored, and we have added an always-on rule in the
+    # first place to override the colour. This is because this color option will
+    # only accept named colours, while you can override the colour in a rule
+    # block with an RGB colour.
+    #
+    # 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)
+    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_thickness      = ${data.plot_format.format_specific.stroke_thickness}
+    layers                = ${data.plot_format.format_specific.layers}
+    thickness             = ${data.plot_format.format_specific.thickness}
+    padding               = ${data.plot_format.format_specific.padding}
+    margin                = ${data.plot_format.format_specific.margin}u
+    layers_overflow       = ${data.plot_format.format_specific.overflow.overflow_behavior}
+    #if str($data.plot_format.format_specific.overflow.overflow_behavior) != "hide":
+    layers_overflow_color = $circosColor($data.plot_format.format_specific.overflow.layer_overflow_color)
+    #end if
+#else if str($plot_type) == 'text':
+    type           = ${plot_type}
+  #if $data.plot_format.format_specific.link.show_link == "yes":
+    show_links     = yes
+    link_dims      = ${data.plot_format.format_specific.link.link_dims}
+    link_thickness = ${data.plot_format.format_specific.link.link_thickness}p
+    link_color     = ${data.plot_format.format_specific.link.link_color}
+  #else
+    show_links     = no
+  #end if
+
+  #if $data.plot_format.format_specific.snuggle.label_snuggle == "yes":
+    label_snuggle                  = ${data.plot_format.format_specific.snuggle.label_snuggle}
+    max_snuggle_distance           = ${data.plot_format.format_specific.snuggle.max_snuggle_distance}r
+    snuggle_sampling               = ${data.plot_format.format_specific.snuggle.snuggle_sampling}
+    snuggle_tolerance              = ${data.plot_format.format_specific.snuggle.snuggle_tolerance}r
+    snuggle_link_overlap_test      = ${data.plot_format.format_specific.snuggle.snuggle_link_overlap_test}
+    snuggle_link_overlap_tolerance = ${data.plot_format.format_specific.snuggle.snuggle_link_overlap_tolerance}p
+    snuggle_refine = ${data.plot_format.format_specific.snuggle.snuggle_refine}
+  #end if
+
+    label_size     = ${data.plot_format.format_specific.label_size}p
+    label_font     = condensed
+    padding        = 0p
+    rpadding       = 0p
+#end if
+
+    <rules>
+    #if str($plot_type) == 'scatter':
+        <rule>
+            # Workaround for above commented colour bug.
+            condition  = 1
+            fill_color = $circosColor($data.plot_format.format_specific.fill_color)
+            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":
+                    condition = 1
+                #elif str($condition.application.application_select) == "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:
+                    condition = var(start) > $condition.application.pos_gt
+                    #end if
+
+                    #if $condition.application.pos_lt:
                     condition = var(start) < $condition.application.pos_lt
                     #end if
                 #elif str($condition.application.application_select) == "value":
-                    #if float($condition.application.pos_gt) != 0:
+                    #if $condition.application.pos_gt:
                     condition = var(value) > $condition.application.pos_gt
                     #end if
 
-                    #if float($condition.application.pos_lt) != 0:
+                    #if $condition.application.pos_lt:
                     condition = var(value) < $condition.application.pos_lt
                     #end if
                 #elif str($condition.application.application_select) == "var":
@@ -169,9 +362,19 @@
                     #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) == 'histogram' else "color"
+                    #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}, ${x_max})))
+                #elif str($action.action.action_select) in ('fill_color', 'stroke_color'):
+                    #if str($plot_type) in ('tile', ):
+                        color = $circosColor($action.action.action_value)
+                    #else:
+                        #if str($action.action.action_select) == "stroke_color" and str($plot_type) == "histogram":
+                        color = $circosColor($action.action.action_value)
+                        #else
+                        $action.action.action_select = $circosColor($action.action.action_value)
+                        #end if
+                    #end if
                 #else
                     $action.action.action_select = ${action.action.action_value}
                 #end if
@@ -203,44 +406,39 @@
     </backgrounds>
 </plot>
 #end for
+</plots>
     ]]></configfile>
   </xml>
 
   <xml name="configfile_links_conf">
     <configfile name="links_conf"><![CDATA[
+@UTILS@
+<links>
 #for $hi, $data in enumerate($sec_links.data):
 <link>
-    #def circosColor($value)
-        #set $value = str($value)
-        #set $r = int($value[1:3], 16)
-        #set $g = int($value[3:5], 16)
-        #set $b = int($value[5:], 16)
-        $r, $g, $b
-    #end def
-
-    file = data/links-${hi}.txt
-
-    radius   = ${data.radius}r
-    ribbon   = ${data.linktype.ribbon}
-    #if $data.linktype.ribbon == 'yes'
-        ${data.linktype.twist}
-    #end if
-    color                = $circosColor($data.color)
+    file                 = data/links-${hi}.txt
+    radius               = ${data.radius}r
+    ribbon               = ${data.linktype.ribbon}
+  #if $data.linktype.ribbon == 'yes'
+    ${data.linktype.twist}
+   #if $data.linktype.pattern != 'solid':
+    pattern              = ${data.linktype.pattern}
+   #end if
+  #end if
+    color                = $circosColorAlpha($data.color, $data.color_alpha)
     bezier_radius        = ${data.bezier_radius}r
     thickness            = ${data.thickness}
     crest                = ${data.advanced.crest}
     bezier_radius_purity = ${data.advanced.bezier_radius_purity}
-
-    #if $data.advanced.perturbation.perturb == 'yes'
-        perturb = yes
-        perturb_crest = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
-        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
+  #if $data.advanced.perturbation.perturb == 'yes'
+    perturb                      = yes
+    perturb_crest                = ${data.advanced.perturbation.perturb_crest_min},${data.advanced.perturbation.perturb_crest_max}
+    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 $data.sec_link_rule.rules:
@@ -251,6 +449,8 @@
                     condition = var($cond)
                 #elif $cond == 'always'
                     condition = 1
+                #elif $cond == 'random'
+                    condition = rand() < ${condition.application.value}
                 #else
                     #set op = $condition.application.comparison.compare
                     #set val = $condition.application.comparison.compval
@@ -258,6 +458,8 @@
                         #if $op == 'between' or $op == 'fromto'
                             #set val2 = $condition.application.comparison.compval2
                             #set c=''.join([str($op),"(",str($val),",",str($val2),")"])
+                        #elif $op == 'on'
+                            #set c='(var(chr1) eq "%s" or var(chr2) eq "%s")' % (str($val), str($val))
                         #else
                             #set c=''.join([str($op),"(",str($val),")"])
                         #end if
@@ -280,7 +482,7 @@
                 #set actiontype = $action.action.action_select
                 #if $actiontype == 'color':
                     #if $action.action.dynamic.dynamic_select == "static":
-                        #set actionval = $circosColor($action.action.dynamic.action_value)
+                        #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
@@ -312,113 +514,11 @@
     </rules>
 </link>
 #end for
+</links>
     ]]></configfile>
   </xml>
 
   <xml name="test_case">
-    <configfile name="test_case_conf"><![CDATA[
-<!--
-mkdir -p test-data/my-test-case/ &&
-#if $reference_genome.reference_genome_source == 'history':
-    cp '${genome_fasta}' test-data/my-test-case/input.fa &&
-#end if
-
-#if $reference_genome.reference_genome_source != 'karyotype':
-#if $reference_genome.bands:
-cp '${reference_genome.bands}' test-data/my-test-case/bands.${reference_genome.bands.ext} &&
-#end if
-#end if
-
-#for $idx, $data in enumerate($sec_tdd.data):
-    #if str($data.plot_format.plot_format_select) in ('histogram', 'heatmap'):
-        #for $jdx, $file in enumerate($data.plot_format.data_source):
-cp '${file}' test-data/my-test-case/${idx}-${jdx}.${file.ext} &&
-        #end for
-    #else
-cp '${data.plot_format.data_source}' test-data/my-test-case/${idx}.${data.plot_format.data_source.ext} &&
-    #end if
-#end for
-cp "$output_png" test-data/my-test-case/output.png &&
-cp "$output_svg" test-data/my-test-case/output.svg &&
--->
-<test>
-    <param name="reference_genome|reference_genome_source" value="${reference_genome.reference_genome_source}"/>
-    <param name="reference_genome|genome_fasta" value="my-test-case/input.fa" />
-    <!-- ideograms -->
-    <param name="ideogram|spacing" value="${ideogram.spacing}" />
-    <param name="ideogram|radius" value="${ideogram.radius}" />
-    <param name="ideogram|thickness" value="${ideogram.thickness}" />
-    <param name="ideogram|ideogram_labels|show_label" value="${ideogram.ideogram_labels.show_label}" />
-    <param name="ideogram|ideogram_labels|parallel" value="${ideogram.ideogram_labels.parallel}" />
-    #if $reference_genome.reference_genome_source != 'karyotype':
-    #if $reference_genome.bands:
-    <param name="reference_genome.bands" value="my-test-case/bands.${reference_genome.bands.ext}" />
-    #end if
-    #end if
-    <!-- Ticks -->
-    <param name="ticks|show_ticks" value="${ticks.show_ticks}" />
-    <param name="ticks|radius" value="${ticks.radius}" />
-    <param name="ticks|color" value="${ticks.color}" />
-    <param name="ticks|multiplier" value="${ticks.multiplier}" />
-    #for $idx, $tick_group in enumerate($ticks.tick_group):
-    <param name="ticks|tick_group_${idx}|tickspacing" value="${tick_group.spacing}" />
-    <param name="ticks|tick_group_${idx}|size" value="${tick_group.size}" />
-    <param name="ticks|tick_group_${idx}|show_tick_labels" value="${tick_group.show_tick_labels}" />
-    <param name="ticks|tick_group_${idx}|label_size" value="${tick_group.label_size}" />
-    <param name="ticks|tick_group_${idx}|label_offset" value="${tick_group.label_offset}" />
-    <param name="ticks|tick_group_${idx}|label_format" value="${tick_group.format}" />
-    #end for
-    <!-- Data -->
-    #for $idx, $data_group in enumerate($sec_tdd.data):
-    <param name="sec_tdd|data_${idx}|r0" value="${data_group.r0}" />
-    <param name="sec_tdd|data_${idx}|r1" value="${data_group.r1}" />
-    <param name="sec_tdd|data_${idx}|orientation" value="${data_group.orientation}" />
-    <param name="sec_tdd|data_${idx}|plot_format|plot_format_select" value="${data_group.plot_format.plot_format_select}" />
-        <!-- Note, please double check your files -->
-    #if str($data_group.plot_format.plot_format_select) == 'histogram':
-        #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
-        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|extend_bins" value="${data_group.plot_format.format_specific.extend_bins}" />
-    #else if str($data_group.plot_format.plot_format_select) == 'heatmap':
-        #set my_files = ','.join([ "my-test-case/%s-%s.%s" % ($idx, $j, $file.ext) for ($j, $file) in enumerate($data_group.plot_format.data_source)])
-        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="${my_files}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|scale_log_base" value="${data_group.plot_format.format_specific.scale_log_base}" />
-    #else if str($data_group.plot_format.plot_format_select) == 'line':
-        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke" value="${data_group.plot_format.format_specific.stroke}" />
-    #else if str($data_group.plot_format.plot_format_select) == 'scatter':
-        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph" value="${data_group.plot_format.format_specific.glyph}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|glyph_size" value="${data_group.plot_format.format_specific.glyph_size}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_min" value="${data_group.plot_format.format_specific.data_min}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|data_max" value="${data_group.plot_format.format_specific.data_max}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_color" value="${data_group.plot_format.format_specific.stroke_color}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
-    #else if str($data_group.plot_format.plot_format_select) == 'tile':
-        <param name="sec_tdd|data_${idx}|plot_format|data_source" value="my-test-case/${idx}.${data.plot_format.data_source.ext}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|fill_color" value="${data_group.plot_format.format_specific.fill_color}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|color" value="${data_group.plot_format.format_specific.color}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|stroke_thickness" value="${data_group.plot_format.format_specific.stroke_thickness}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|layers" value="${data_group.plot_format.format_specific.layers}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|thickness" value="${data_group.plot_format.format_specific.thickness}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|padding" value="${data_group.plot_format.format_specific.padding}" />
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|overflow_behavior" value="${data_group.plot_format.format_specific.overflow.overflow_behavior}" />
-        #if str($data_group.plot_format.format_specific.overflow.overflow_behavior) != 'hide':
-        <param name="sec_tdd|data_${idx}|plot_format|format_specific|overflow|layer_overflow_color" value="${data_group.plot_format.format_specific.overflow.layer_overflow_color}" />
-        #end if
-    #end if
-    ## Next line intentionally blank
-
-    #end for
-
-    <!-- Outputs -->
-    <output name="output_png" file="my-test-case/output.png" />
-    <output name="output_svg" file="my-test-case/output.svg" />
-</test>
-    ]]></configfile>
+    <inputs name="test_case_conf" />
   </xml>
 </macros>