# HG changeset patch
# User eric-rasche
# Date 1497126061 14400
# Node ID eb3af6e9f6337f60e764bd64a18bd95802c8b43e
# Parent  b72f2db6d4176e633d2dd8ad0747771366be5f6c
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit 3ac672baa4a93250828fd4a450cb5689b0b03474

diff -r b72f2db6d417 -r eb3af6e9f633 circgraph.xml
--- a/circgraph.xml	Sat Jun 10 14:16:41 2017 -0400
+++ b/circgraph.xml	Sat Jun 10 16:21:01 2017 -0400
@@ -24,8 +24,8 @@
                 genomeref.fa
             #end if
 
-            #if $ideogram.bands:
-                "${ideogram.bands}"
+            #if $reference_genome.bands:
+                "${reference_genome.bands}"
             #end if
         > circos/conf/karyotype.txt &&
     #else
diff -r b72f2db6d417 -r eb3af6e9f633 macros.xml
--- a/macros.xml	Sat Jun 10 14:16:41 2017 -0400
+++ b/macros.xml	Sat Jun 10 16:21:01 2017 -0400
@@ -182,11 +182,13 @@
                         <expand macro="brewer_scale" name="action_value" label="Fill Color"/>
                         <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
                         <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
+                        <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
                     </when>
                     <when value="color_value">
                         <expand macro="brewer_scale" name="action_value" label="Stroke Color"/>
                         <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
                         <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
+                        <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
                     </when>
                 </conditional>
             </repeat>
@@ -281,6 +283,7 @@
                                 <expand macro="brewer_scale" label="Fill Color" name="action_value"/>
                                 <param name="min_value" type="float" value="-1" label="Expected minimum value of dataset"/>
                                 <param name="max_value" type="float" value="1" label="Expected maximum value of dataset"/>
+                                <param name="invert" type="boolean" truevalue="True" falsevalue="False" label="Invert Color Scale" />
                             </when>
                         </conditional>
                     </when>
diff -r b72f2db6d417 -r eb3af6e9f633 macros_conffiles.xml
--- a/macros_conffiles.xml	Sat Jun 10 14:16:41 2017 -0400
+++ b/macros_conffiles.xml	Sat Jun 10 16:21:01 2017 -0400
@@ -166,12 +166,13 @@
             #end for
 
             #for $action in $rule.actions:
-                #set x_fill_color = $action.action.action_value
-                #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + 1
-                #set x_fill_color_qw = ' '.join(["%s-%s" % ($action.action.action_value, $i) for i in range(1, $x_fill_color_count)])
+                #if str($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
 
-                #if str($action.action.action_select) == "fill_color_value" or str($action.action.action_select) == "color_value" :
-                    fill_color = eval(qw(${x_fill_color_qw})[remap_int(var(value), ${action.action.min_value}, ${action.action.max_value}, 0, ${x_fill_color_count - 1})])
+                    fill_color = eval(sprintf("${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 = ${action.action.action_value}
                 #end if
@@ -284,9 +285,11 @@
                         $actiontype = $actionval
                     #else
                         #set x_fill_color = $action.action.dynamic.action_value
-                        #set x_fill_color_count = int(str($x_fill_color).split('-')[1]) + 1
-                        #set x_fill_color_qw = ' '.join(["%s-%s" % ($action.action.dynamic.action_value, $i) for i in range(1, $x_fill_color_count)])
-                        $actiontype = eval(qw(${x_fill_color_qw})[remap_int(var(value), ${action.action.dynamic.min_value}, ${action.action.dynamic.max_value}, 0, ${x_fill_color_count - 1})])
+                        #set x_fill_color_count = int(str($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})))
                     #end if
                 #else
                     #set actionval = $action.action.action_value
@@ -342,9 +345,13 @@
 #if $reference_genome.reference_genome_source == 'history':
     cp ${genome_fasta} test-data/my-test-case/input.fa;
 #end if
-#if $ideogram.bands:
-cp ${ideogram.bands} test-data/my-test-case/bands.${ideogram.bands.ext};
+
+#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):
@@ -366,8 +373,10 @@
     <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 $ideogram.bands:
-    <param name="ideogram|bands" value="my-test-case/bands.${ideogram.bands.ext}" />
+    #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}" />