--- a/circos.xml	Fri May 01 11:28:11 2020 +0000
+++ b/circos.xml	Mon May 25 14:50:52 2020 +0000
@@ -29,7 +29,7 @@
 #end if
 
 #if $reference_genome.ref.ref_source in ('lengths', 'cached'):
-    python '$__tool_directory__/genome-lengths-to-karyotype.py'
+    python '$__tool_directory__/karyotype-from-lengths.py'
         #if $reference_genome.ref.ref_source == 'lengths':
             ${reference_genome.ref.input_lengths}'
         #else
@@ -41,22 +41,22 @@
                 <(head -n 50 '${reference_genome.ref.fasta_indexes.fields.len_path}')
             #end if
         #end if
-        '${reference_genome.ref.color}'
         > circos/conf/karyotype.txt &&
 #else if $reference_genome.ref.ref_source == 'karyotype':
     cp $reference_genome.ref.input_karyotype circos/conf/karyotype.txt &&
 #else if str($reference_genome.ref.ref_source) == 'history':
     ## Process the karyotype.txt file
     python
-        '$__tool_directory__/fasta-to-karyotype.py'
+        '$__tool_directory__/karyotype-from-fasta.py'
         genomeref.fa
-        '${reference_genome.ref.color}'
-
-    > circos/conf/karyotype.txt &&
+        > circos/conf/karyotype.txt &&
 #else if $reference_genome.ref.ref_source == 'preset':
     cp '$__tool_directory__/karyotype/'${reference_genome.ref.preset_karyotype} circos/conf/karyotype.txt &&
 #end if
 
+python '$__tool_directory__/karyotype-colors.py' `grep -c '^chr\s' 'circos/conf/karyotype.txt'`
+    > 'circos/conf/karyotype-colors.conf' &&
+
 touch circos/conf/karyotype-colors.conf &&
 
 ## #if $ideogram.bands.bands:
@@ -158,18 +158,15 @@
                     <param name="fasta_indexes" type="select" label="Source Genome Build" help="Warning: this also contains unplaced scaffolds present in the reference genome. You can restrict the regions to plot in 'Limit/Filter Chromosomes' below, or supply your own file.">
                         <options from_data_table="__dbkeys__"/>
                     </param>
-                    <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/>
                 </when>
                 <when value="history">
                     <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
-                    <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/>
                 </when>
                 <when value="karyotype">
                     <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration" help="Provide your own karyotype configuration. Should be 'chr - ID LABEL START END COLOR'"/>
                 </when>
                 <when value="lengths">
                     <param name="input_lengths" type="data" format="tabular" label="Sequence Lengths" help="This needs to be a 2+ column tabular, e.g. from 'Compute sequence lengths', the first column should be chromosome and second should be length."/>
-                    <expand macro="brewer_scale" name="color" label="Ideogram Color Scheme" help="This will apply a color scheme to the generated karyotype file"/>
                 </when>
             </conditional>
         </section>