# HG changeset patch
# User iuc
# Date 1685087695 0
# Node ID 59fd173ac850c08372d5175efcde755aa0a3c5cb
# Parent  360df4999907d39a61da7559bceada9693344eb4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit b0607963d6cf57fef81c5468e0af914430e7d35b

diff -r 360df4999907 -r 59fd173ac850 macros.xml
--- a/macros.xml	Tue Mar 28 10:48:50 2023 +0000
+++ b/macros.xml	Fri May 26 07:54:55 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">3.8</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement>
@@ -59,7 +59,7 @@
         <param name="track_input_bedgraph_matrix" type="data" format="bedgraph" label="Track file(s) bedgraph format" multiple="True"/>
     </xml>
     <xml name="track_input_link_macro">
-        <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="False"/>
+        <param name="track_input_link" type="data" format="bed,interval" label="Track file(s) for links" multiple="True"/>
     </xml>
     <xml name="track_input_fasta_macro">
         <conditional name="fasta_source">
diff -r 360df4999907 -r 59fd173ac850 pyGenomeTracks.xml
--- a/pyGenomeTracks.xml	Tue Mar 28 10:48:50 2023 +0000
+++ b/pyGenomeTracks.xml	Fri May 26 07:54:55 2023 +0000
@@ -188,6 +188,14 @@
 color = bed_rgb
       #elif $track.track_file_style_conditional.color_bed.color:
 color = $track.track_file_style_conditional.color_bed.color
+        #if $track.track_file_style_conditional.color_bed.color_bed_select == "colormap":
+          #if str($track.track_file_style_conditional.color_bed.min_value) != '':
+min_value = $track.track_file_style_conditional.color_bed.min_value
+          #end if
+          #if str($track.track_file_style_conditional.color_bed.max_value) != '':
+max_value = $track.track_file_style_conditional.color_bed.max_value
+          #end if
+        #end if
       #end if
       #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
 border_color = $track.track_file_style_conditional.border_color_bed.color
@@ -230,6 +238,14 @@
 color = bed_rgb
       #elif $track.track_file_style_conditional.color_bed.color:
 color = $track.track_file_style_conditional.color_bed.color
+        #if $track.track_file_style_conditional.color_bed.color_bed_select == "colormap":
+          #if str($track.track_file_style_conditional.color_bed.min_value) != '':
+min_value = $track.track_file_style_conditional.color_bed.min_value
+          #end if
+          #if str($track.track_file_style_conditional.color_bed.max_value) != '':
+max_value = $track.track_file_style_conditional.color_bed.max_value
+          #end if
+        #end if
       #end if
       #if $track.track_file_style_conditional.border_color_bed.border_color_bed_select == 'manually':
 border_color = $track.track_file_style_conditional.border_color_bed.color
@@ -305,47 +321,49 @@
 
   ## Link
   #if $track.track_file_style_conditional.track_file_style_selector == "link_track_option":
-[links_$counter]
-file = $track.track_file_style_conditional.track_input_link
-    #if $track.track_file_style_conditional.title:
+    #for $counter_link, $data_link in enumerate($track.track_file_style_conditional.track_input_link):
+[links_${counter}_${counter_link}]
+file = $data_link
+      #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
-    #elif $track.track_file_style_conditional.overlay_select == 'no':
-title = $track.track_file_style_conditional.track_input_link.element_identifier
-    #end if
-    #if $track.track_file_style_conditional.height:
+      #elif $track.track_file_style_conditional.overlay_select == 'no':
+title = $data_link.element_identifier
+      #end if
+      #if $track.track_file_style_conditional.height:
 height = $track.track_file_style_conditional.height
-    #end if
-    #if $track.track_file_style_conditional.min_value != "":
+      #end if
+      #if $track.track_file_style_conditional.min_value != "":
 min_value = $track.track_file_style_conditional.min_value
-    #end if
-    #if $track.track_file_style_conditional.max_value != "":
+      #end if
+      #if $track.track_file_style_conditional.max_value != "":
 max_value = $track.track_file_style_conditional.max_value
-    #end if
+      #end if
 color = $track.track_file_style_conditional.color_link.color
 alpha = $track.track_file_style_conditional.alpha
 line_width = $track.track_file_style_conditional.line_width
 line_style = $track.track_file_style_conditional.line_style
 links_type = $track.track_file_style_conditional.display.links_type
-    #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']:
+      #if $track.track_file_style_conditional.display.links_type in ['arcs', 'triangles']:
 compact_arcs_level = $track.track_file_style_conditional.display.compact_arcs_level
 use_middle = $track.track_file_style_conditional.display.use_middle
-    #end if
-    #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "":
+      #end if
+      #if $track.track_file_style_conditional.display.links_type != 'squares' and $track.track_file_style_conditional.display.ylim != "":
 ylim = $track.track_file_style_conditional.display.ylim
-    #end if
-    #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "":
+      #end if
+      #if $track.track_file_style_conditional.display.links_type == 'squares' and $track.track_file_style_conditional.display.region2 != "":
 region2 = $track.track_file_style_conditional.display.region2
-    #end if
-    #if $track.track_file_style_conditional.invert_orientation:
+      #end if
+      #if $track.track_file_style_conditional.invert_orientation:
 orientation = inverted
-    #end if
+      #end if
 overlay_previous = $track.track_file_style_conditional.overlay_select
 file_type = links
-    ## If spacer is asked a new section is created:
-    #if $track.track_file_style_conditional.spacer_height != "":
+      ## If spacer is asked a new section is created:
+      #if $track.track_file_style_conditional.spacer_height != "":
 [spacer]
 height = $track.track_file_style_conditional.spacer_height
-    #end if
+      #end if
+    #end for
   #end if
 
   ## Narrow peak
@@ -889,6 +907,7 @@
                                 <option value="viridis">viridis</option>
                                 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
                             </param>
+                            <expand macro="minmax_macro" />
                         </when>
                     </conditional>
                     <expand macro="border_color_bed_macro" />
@@ -919,6 +938,7 @@
                                 <option value="viridis">viridis</option>
                                 <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
                             </param>
+                            <expand macro="minmax_macro" />
                         </when>
                     </conditional>
                     <expand macro="border_color_bed_macro" />
@@ -1748,6 +1768,8 @@
                     <conditional name="color_bed">
                         <param name="color_bed_select" value="colormap" />
                         <param name="color" value="RdYlBu_r" />
+                        <param name="min_value" value="0" />
+                        <param name="max_value" value="2" />
                     </conditional>
                 </conditional>
             </repeat>
@@ -2428,7 +2450,7 @@
             <repeat name="tracks">
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="link_track_option" />
-                    <param name="track_input_link" value="test.arcs" ftype="bed" />
+                    <param name="track_input_link" value="test.arcs,test.arcs" ftype="bed" />
                     <param name="title" value="highly compacted" />
                     <conditional name="color_link">
                         <param name="color_link_select" value="manually" />
diff -r 360df4999907 -r 59fd173ac850 test-data/master_TADs_BW_plot.png
Binary file test-data/master_TADs_BW_plot.png has changed
diff -r 360df4999907 -r 59fd173ac850 test-data/test13.ini
--- a/test-data/test13.ini	Tue Mar 28 10:48:50 2023 +0000
+++ b/test-data/test13.ini	Fri May 26 07:54:55 2023 +0000
@@ -35,7 +35,7 @@
 compact_arcs_level = 1
 overlay_previous = no
 file_type = links
-[links_4]
+[links_4_0]
 file = test.arcs
 title = highly compacted
 height = 1.5
@@ -47,3 +47,15 @@
 compact_arcs_level = 2
 overlay_previous = no
 file_type = links
+[links_4_1]
+file = test.arcs
+title = highly compacted
+height = 1.5
+color = #000000
+alpha = 1.0
+line_width = 0.5
+line_style = solid
+links_type = arcs
+compact_arcs_level = 2
+overlay_previous = no
+file_type = links
diff -r 360df4999907 -r 59fd173ac850 test-data/test3.ini
--- a/test-data/test3.ini	Tue Mar 28 10:48:50 2023 +0000
+++ b/test-data/test3.ini	Fri May 26 07:54:55 2023 +0000
@@ -147,6 +147,8 @@
 line_width = 0.5
 arrowhead_included = false
 overlay_previous = no
+min_value = 0
+max_value = 2
 [genes_12_0]
 file = test-data/domains.bed
 title = domains.bed using the 9th field for colors interleaved border=red
diff -r 360df4999907 -r 59fd173ac850 test-data/test_link2.png
Binary file test-data/test_link2.png has changed