# HG changeset patch
# User eric-rasche
# Date 1497116312 14400
# Node ID 169adf243c0ad03d60e58eb23232f158480cf23a
# Parent  b25b3518c2ce153e12b776c25afa0dfce9a30337
planemo upload for repository https://github.com/TAMU-CPT/galaxy-circos-tool commit ee1fa2dab456c14a2538eb66033614e14a21a2ec

diff -r b25b3518c2ce -r 169adf243c0a circgraph.xml
--- a/circgraph.xml	Sat Jun 10 12:55:28 2017 -0400
+++ b/circgraph.xml	Sat Jun 10 13:38:32 2017 -0400
@@ -14,20 +14,23 @@
         ln -s $reference_genome.genome_fasta genomeref.fa;
     #end if
 
-    ## Process the karyotype.txt file
-    python $__tool_directory__/fasta-to-karyotype.py
+    #if $reference_genome.reference_genome_source != 'karyotype':
+        ## Process the karyotype.txt file
+        python $__tool_directory__/fasta-to-karyotype.py
 
-        #if str($reference_genome.reference_genome_source) == 'cached':
-            "${reference_genome.fasta_indexes.fields.path}"
-        #else if str($reference_genome.reference_genome_source) == 'history':
-            genomeref.fa
-        #end if
+            #if str($reference_genome.reference_genome_source) == 'cached':
+                "${reference_genome.fasta_indexes.fields.path}"
+            #else if str($reference_genome.reference_genome_source) == 'history':
+                genomeref.fa
+            #end if
 
-        #if $ideogram.bands:
-            "${ideogram.bands}"
-        #end if
-
-    > circos/conf/karyotype.txt &&
+            #if $ideogram.bands:
+                "${ideogram.bands}"
+            #end if
+        > circos/conf/karyotype.txt &&
+    #else
+        cp $reference_genome.input_karyotype circos/conf/karyotype.txt &&
+    #end if
 
     mv $circos_conf circos/conf/circos.conf &&
     mv $ticks_conf circos/conf/ticks.conf &&
@@ -82,14 +85,24 @@
         <param name="reference_genome_source" type="select" label="Reference Genome">
             <option value="history" selected="True">From History</option>
             <option value="cached">Locally Cached</option>
+            <option value="karyotype">Karyotype</option>
         </param>
         <when value="cached">
             <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
                 <options from_data_table="all_fasta"/>
             </param>
+            <!-- TODO: multiple band files? -->
+            <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
+                   help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
         </when>
         <when value="history">
             <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
+            <!-- TODO: multiple band files? -->
+            <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
+                   help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
+        </when>
+        <when value="karyotype">
+            <param name="input_karyotype" type="data" format="tabular,txt" label="Karyotype Configuration"/>
         </when>
     </conditional>
 
@@ -105,9 +118,6 @@
             <param name="parallel" type="boolean" label="Parallel" truevalue="yes" falsevalue="no"
                  help="When set to yes/true, labels will be perpendicular to the tangent of the circle at the location of the label. Otherwise, they will be parallel with the tangent of the circle"/>
         </section>
-        <!-- TODO: multiple band files? -->
-        <param name="bands" type="data" format="bed6,bed12" optional="true" label="Cytogenetic Bands"
-             help="If defined, will display cytogenetic bands as part of the karyotype configuration"/>
     </section>
 
     <section name="ticks" title="Ticks">
diff -r b25b3518c2ce -r 169adf243c0a macros.xml
--- a/macros.xml	Sat Jun 10 12:55:28 2017 -0400
+++ b/macros.xml	Sat Jun 10 13:38:32 2017 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@WRAPPER_VERSION@">0.9-RC1</token>
+  <token name="@WRAPPER_VERSION@">0.9-RC2</token>
   <xml name="requirements">
       <requirements>
         <requirement type="package" version="0.69.4">circos</requirement>
@@ -202,6 +202,7 @@
             <repeat name="conditions" title="Conditions to Apply" help="Multiple conditions will be combined using AND">
                 <conditional name="application">
                     <param name="application_select" type="select" label="Condition">
+                        <option value="always">True / Always Applied</option>
                         <option value="interchr">Interchromosomal</option>
                         <option value="intrachr">Intrachromosomal</option>
                         <option value="chr">Chromosome</option>
@@ -253,6 +254,7 @@
                     <when value="inv"/>
                     <when value="interchr"/>
                     <when value="intrachr"/>
+                    <when value="always"/>
                 </conditional>
             </repeat>
             <repeat name="actions" title="Actions to Apply">
@@ -267,7 +269,20 @@
                         <param name="action_value" type="boolean" label="Show" truevalue="yes" falsevalue="no"/>
                     </when>
                     <when value="color">
-                        <expand macro="circos_color" label="Link Color" name="action_value"/>
+                        <conditional name="dynamic">
+                            <param name="dynamic_select" type="select" label="Static / Dynamic Change">
+                                <option value="static">Static: Change is always applied</option>
+                                <option value="dynamic">Dynamic: Change is sometimes applied</option>
+                            </param>
+                            <when value="static">
+                                <expand macro="circos_color" label="Link Color" name="action_value"/>
+                            </when>
+                            <when value="dynamic">
+                                <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"/>
+                            </when>
+                        </conditional>
                     </when>
                     <when value="thickness">
                         <param name="action_value" type="integer" value="1" label="Thickness"/>
diff -r b25b3518c2ce -r 169adf243c0a macros_conffiles.xml
--- a/macros_conffiles.xml	Sat Jun 10 12:55:28 2017 -0400
+++ b/macros_conffiles.xml	Sat Jun 10 13:38:32 2017 -0400
@@ -249,6 +249,8 @@
                 #set cond = $condition.application.application_select
                 #if $cond == 'interchr' or $cond == 'intrachr' or $cond == 'inv' or $cond == 'rev'
                     condition = var($cond)
+                #elif $cond == 'always'
+                    condition = 1
                 #else
                     #set op = $condition.application.comparison.compare
                     #set val = $condition.application.comparison.compval
@@ -278,9 +280,18 @@
                 #set actiontype = $action.action.action_select
                 #set actionval = $action.action.action_value
                 #if $actiontype == 'color':
-                    #set actionval = $circosColor($actionval)
+                    #if $action.action.dynamic.dynamic_select == "static":
+                        #set actionval = $circosColor($actionval)
+                        $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})])
+                    #end if
+                #else
+                    $actiontype = $actionval
                 #end if
-                $actiontype = $actionval
             #end for
 
             $rule.continue_flow