# HG changeset patch
# User iuc
# Date 1644792225 0
# Node ID a1abfa420d9d096bb8fbe462dde0e24dd1a004c0
# Parent  2824d77cd8f874499e7f18b10915f9679b2b20a8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks commit 5bd033a726b088eef3cf591da36ca1e9ba70d8c7"

diff -r 2824d77cd8f8 -r a1abfa420d9d macros.xml
--- a/macros.xml	Wed Nov 18 21:33:46 2020 +0000
+++ b/macros.xml	Sun Feb 13 22:43:45 2022 +0000
@@ -1,9 +1,9 @@
 <macros>
-    <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
-    <token name="@WRAPPER_VERSION@">3.6</token>
+    <token name="@TOOL_VERSION@">3.6</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">pygenometracks</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement>
             <yield />
         </requirements>
         <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>
@@ -204,7 +204,7 @@
             <option value="dashdot">Dashdot</option>
         </param>
     </xml>
-    <xml name="colormap_macro">
+    <xml name="colormap_macro_noRdYlBu_r_noViridis">
         <option value="RdYlBu">RdYlBu</option>
         <option value="Accent">Accent</option>
         <option value="Spectral">Spectral</option>
@@ -274,7 +274,6 @@
         <option value="brg">brg</option>
         <option value="jet">jet</option>
         <option value="afmhot">afmhot</option>
-        <option value="viridis">viridis</option>
         <option value="plasma">plasma</option>
         <option value="inferno">inferno</option>
         <option value="magma">magma</option>
@@ -328,7 +327,6 @@
         <option value="RdPu_r">RdPu reversed</option>
         <option value="YlGn_r">YlGn reversed</option>
         <option value="PuBuGn_r">PuBuGn reversed</option>
-        <option value="RdYlBu_r">RdYlBu reversed</option>
         <option value="RdYlGn_r">RdYlGn reversed</option>
         <option value="YlGnBu_r">YlGnBu reversed</option>
         <option value="YlOrBr_r">YlOrBr reversed</option>
diff -r 2824d77cd8f8 -r a1abfa420d9d pyGenomeTracks.xml
--- a/pyGenomeTracks.xml	Wed Nov 18 21:33:46 2020 +0000
+++ b/pyGenomeTracks.xml	Sun Feb 13 22:43:45 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="pygenomeTracks" name="@BINARY@" version="@WRAPPER_VERSION@">
+<tool id="pygenomeTracks" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>plot genomic data tracks</description>
     <macros>
         <token name="@BINARY@">pyGenomeTracks</token>
@@ -56,7 +56,7 @@
       #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
       #else:
-title = $data_matrix.name
+title = $data_matrix.element_identifier
       #end if
       #if $track.track_file_style_conditional.depth:
 depth = $track.track_file_style_conditional.depth
@@ -114,7 +114,7 @@
       #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
       #else:
-title = $data_bed.name
+title = $data_bed.element_identifier
       #end if
       #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
 color = bed_rgb
@@ -153,7 +153,7 @@
       #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
       #elif $track.track_file_style_conditional.overlay_select == 'no':
-title = $data_bed.name
+title = $data_bed.element_identifier
       #end if
       #if $track.track_file_style_conditional.color_bed.color_bed_select == "bed_rgb":
 color = bed_rgb
@@ -226,7 +226,7 @@
     #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.name
+title = $track.track_file_style_conditional.track_input_link.element_identifier
     #end if
     #if $track.track_file_style_conditional.height:
 height = $track.track_file_style_conditional.height
@@ -267,7 +267,7 @@
       #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
       #elif $track.track_file_style_conditional.overlay_select == 'no':
-title = $data_narrow_peak.name
+title = $data_narrow_peak.element_identifier
       #end if
 color = $track.track_file_style_conditional.color
 type = $track.track_file_style_conditional.display.display_selector
@@ -313,7 +313,7 @@
       #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
       #elif $track.track_file_style_conditional.overlay_select == "no":
-title = $data_bedgraph.name
+title = $data_bedgraph.element_identifier
       #end if
       #if $track.track_file_style_conditional.color:
 color = $track.track_file_style_conditional.color
@@ -388,7 +388,7 @@
       #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
       #elif $track.track_file_style_conditional.overlay_select == "no":
-title = $data_bigwig.name
+title = $data_bigwig.element_identifier
       #end if
       #if $track.track_file_style_conditional.color:
 color = $track.track_file_style_conditional.color
@@ -452,7 +452,7 @@
       #if $track.track_file_style_conditional.title:
 title = $track.track_file_style_conditional.title
       #else:
-title = $data_bedgraph_matrix.name
+title = $data_bedgraph_matrix.element_identifier
       #end if
       #if $track.track_file_style_conditional.height_bedgraph:
 height = $track.track_file_style_conditional.height_bedgraph
@@ -623,13 +623,12 @@
                 <param name="track_file_style_selector" type="select" label="Choose style of the track">
                     <option value="hic_matrix_option">TAD visualization</option>
                     <option value="chrom_states_option">Chromatine states</option>
-                    <option value="bedgraph_matrix_track_option">TAD score</option>
                     <option value="gene_track_option">Gene track / Bed track</option>
                     <option value="link_track_option">Link track</option>
                     <option value="narrow_peak_track_option">NarrowPeak track</option>
                     <option value="bigwig_track_option">Bigwig track</option>
                     <option value="bedgraph_track_option">Bedgraph track </option>
-                    <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
+                    <option value="bedgraph_matrix_track_option">Bedgraph matrix track/TAD score</option>
                     <option value="vlines_track_option">Vlines track</option>
                     <option value="hlines_track_option">Hlines track</option>
                     <option value="spacer_option">Spacer</option>
@@ -642,7 +641,8 @@
 
                     <param name="colormap" type="select" label="Color map to use for the heatmap" help="Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
                         <option value="RdYlBu_r">RdYlBu reversed</option>
-                        <expand macro="colormap_macro"/>
+                        <option value="viridis">viridis</option>
+                        <expand macro="colormap_macro_noRdYlBu_r_noViridis"/>
                     </param>
                     <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
                     <expand macro="minmax_macro" />
@@ -679,7 +679,9 @@
                         <when value="bed_rgb" />
                         <when value="colormap">
                             <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
-                                <expand macro="colormap_macro" />
+                                <option value="RdYlBu_r">RdYlBu reversed</option>
+                                <option value="viridis">viridis</option>
+                                <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
                             </param>
                         </when>
                     </conditional>
@@ -707,7 +709,9 @@
                         <when value="bed_rgb" />
                         <when value="colormap">
                             <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
-                                <expand macro="colormap_macro" />
+                                <option value="RdYlBu_r">RdYlBu reversed</option>
+                                <option value="viridis">viridis</option>
+                                <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
                             </param>
                         </when>
                     </conditional>
@@ -782,7 +786,9 @@
                         </when>
                         <when value="colormap">
                             <param name="color" type="select" label="Color map to use for the scores" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html">
-                                <expand macro="colormap_macro" />
+                                <option value="RdYlBu_r">RdYlBu reversed</option>
+                                <option value="viridis">viridis</option>
+                                <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
                             </param>
                         </when>
                     </conditional>
@@ -936,8 +942,9 @@
                         </when>
                         <when value="matrix">
                             <param name="colormap" type="select" label="colormap">
-                                <option value="viridis">Viridis</option>
-                                <expand macro="colormap_macro" />
+                                <option value="viridis">viridis</option>
+                                <option value="RdYlBu_r">RdYlBu reversed</option>
+                                <expand macro="colormap_macro_noRdYlBu_r_noViridis" />
                             </param>
                         </when>
                     </conditional>