# HG changeset patch
# User iuc
# Date 1578582182 18000
# Node ID 184dfd9e113d053c81f5e633577d7a710ea4eb05
# Parent  fd59d783248af0c48e2e8021f499dc7ba284da93
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit f5db2969e8602eff32ec799d237875b911578fe5"

diff -r fd59d783248a -r 184dfd9e113d circos.xml
--- a/circos.xml	Mon Dec 02 08:14:29 2019 -0500
+++ b/circos.xml	Thu Jan 09 10:03:02 2020 -0500
@@ -331,8 +331,7 @@
                     help="The radial position of the third control point (in addition to the two positions defined by the link coordinates) used to draw the Bezier curve; if this parameter is 0 then straight lines will be used"/>
 
                 <section name="advanced" title="Advanced Settings">
-                    <param name="zdepth" type="float" value="" optional="true" label="Z-depth"
-                        help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple link tracks"/>
+                    <expand macro="zdepth"/>
                     <param name="crest" type="float" value="0.5" min="0" max="1" label="Crest"
                         help="Two additional Bezier control points can be set by using the crest parameter. When defined, points p3 and p4 are added. These points lie at the same angular position as the start and end link termini and have the radial position. In the crest=0 extreme, p3 and p4 are at the same position as p0,p1. In this case, crest has no effect. When crest=1, p3,p4 are at the radial position of p2, the control point set by bezier_radius"/>
                     <param name="bezier_radius_purity" type="float" value="0.75" min="0" max="1" label="Bezier Radius Purity"
@@ -434,7 +433,7 @@
                 <param name="convert_bands" type="boolean" truevalue="yes" falsevalue="no" label="Convert bands from BED format to circos karyotype band format" checked="true"
                 help="Automatically reformat BED file into the appropriate columns. This should be a BED 6+ file, BED 9+ if you want the colours from the BED file automatically used. Otherwise everything will appear grey."/>
                 <param name="fill_bands" type="boolean" truevalue="yes" falsevalue="no" label="Fill Bands" checked="true"/>
-                <param name="band_transparency" type="integer" label="Fill Bands" value="0" min="0" max="5" help="0 is solid, 1 is the least transparent, and 5 is the most transparent"/>
+                <param name="band_transparency" type="integer" label="Band Transparency" value="0" min="0" max="5" help="0 is solid, 1 is the least transparent, and 5 is the most transparent"/>
 
                 <param type="integer" value="2" label="Band Stroke Thickness" name="band_stroke_thickness"/>
                 <expand macro="circos_color" label="Band Stroke Color" name="band_stroke_color" value="#000000"/>
@@ -485,6 +484,8 @@
                 <param name="r0" type="float" value="0.8" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of plot) and 0 (center of the plot)"/>
                 <param name="data_source" type="data" format="tabular,interval" label="Highlight Data Source" help="Columns must be (chrom, start, end)"/>
                 <expand macro="circos_color_alpha" label="Fill Color" name="fill_color" value="#000000"/>
+                <expand macro="stroke_opts"/>
+                <expand macro="zdepth"/>
                 <expand macro="rules" />
             </repeat>
         </section>
diff -r fd59d783248a -r 184dfd9e113d macros.xml
--- a/macros.xml	Mon Dec 02 08:14:29 2019 -0500
+++ b/macros.xml	Thu Jan 09 10:03:02 2020 -0500
@@ -2,7 +2,7 @@
 <macros>
   <token name="@CIRCOS_VERSION@">0.69.8</token>
 
-  <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy2</token>
+  <token name="@WRAPPER_VERSION@">@CIRCOS_VERSION@+galaxy3</token>
 
   <xml name="requirements">
       <requirements>
@@ -141,6 +141,11 @@
     </param>
   </xml>
 
+  <xml name="zdepth">
+    <param name="zdepth" type="float" value="" optional="true" label="Z-depth"
+        help="Optional. Datasets with a higher z-depth value are drawn on top of data sets with a lower value. Only useful if plotting multiple tracks"/>
+  </xml>
+
   <xml name="font_select"
       token_normal="true"
       token_bold="false">
@@ -159,8 +164,8 @@
   <xml name="axes">
     <section name="sec_axes" title="Axes">
         <repeat name="axes" title="Axis">
-            <param name="y0" type="float" value="0" min="0" max="1" label="Inside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/>
-            <param name="y1" type="float" value="1" min="0" max="1" label="Outside Radius" help="Value must be between 1 (outer edge of track) and 0 (inner edge of the track)"/>
+            <param name="y0" type="float" value="0" label="Inside Radius" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y0 should be -10"/>
+            <param name="y1" type="float" value="1" label="Outside Radius" help="Values are according to minimum and maximum values of dataset. E.g. if your dataset goes from -10 to 10, y1 should be 10"/>
 
             <expand macro="circos_color"/>
             <param name="thickness" type="integer" value="1" label="Thickness"/>
@@ -195,7 +200,13 @@
                     <when value="1">
                     </when>
                     <when value="on">
-                        <param name="on_genomes" type="text" label="Comma separated list of contig IDs"/>
+                        <param name="on_genomes" type="text" label="Contig IDs" help="Pipe | separated list of contig IDs">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                  <add value="|" />
+                                </valid>
+                            </sanitizer>
+                        </param>
                     </when>
                     <when value="pos">
                         <param name="pos_gt" type="float" label="Greater than this base" optional="true"/>
@@ -232,7 +243,12 @@
                             </sanitizer>
                         </param>
 
-                        <param name="varvalue" type="text" label="Qualifier value to compare against"/>
+                        <param name="varvalue" type="text" label="Qualifier value to compare against">
+                            <sanitizer>
+                                <valid initial="string.letters,string.digits">
+                                </valid>
+                            </sanitizer>
+                        </param>
                     </when>
                 </conditional>
             </repeat>
diff -r fd59d783248a -r 184dfd9e113d macros_conffiles.xml
--- a/macros_conffiles.xml	Mon Dec 02 08:14:29 2019 -0500
+++ b/macros_conffiles.xml	Thu Jan 09 10:03:02 2020 -0500
@@ -163,10 +163,12 @@
 <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)
+    file             = data/highlight-${hi}.txt # ${data.data_source.element_identifier}
+    r1               = ${data.r1}r
+    r0               = ${data.r0}r
+    fill_color       = $circosColorAlpha($data.fill_color)
+    stroke_color     = $circosColorAlpha($data.stroke_color)
+    stroke_thickness = ${data.stroke_thickness}
 
     <rules>
     #for $rule in $data.sec_rule.rules:
@@ -175,8 +177,7 @@
                 #if str($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 = $on_str
+                    condition = on($condition.application.on_genomes)
                 #elif str($condition.application.application_select) == "pos":
                     #if $condition.application.pos_gt:
                     condition = var(start) > $condition.application.pos_gt
@@ -416,7 +417,7 @@
 <links>
 #for $hi, $data in enumerate($sec_links.data):
 <link>
-    file                 = data/links-${hi}.txt
+    file                 = data/links-${hi}.txt # ${data.data_source.element_identifier}
     radius               = ${data.radius}r
     ribbon               = ${data.linktype.ribbon}
   #if $data.linktype.ribbon == 'yes'