--- a/pyGenomeTracks.xml	Sat Oct 01 08:43:22 2022 +0000
+++ b/pyGenomeTracks.xml	Wed Jan 25 15:33:12 2023 +0000
@@ -581,6 +581,10 @@
 [vlines_$counter]
 file = $track.track_file_style_conditional.track_input_bed_single
 line_width = $track.track_file_style_conditional.line_width
+line_style = $track.track_file_style_conditional.line_style
+color = $track.track_file_style_conditional.color
+alpha = $track.track_file_style_conditional.alpha
+zorder = $track.track_file_style_conditional.zorder
 type = vlines
   #end if
 
@@ -588,8 +592,10 @@
   #if $track.track_file_style_conditional.track_file_style_selector == "vhighlight_track_option":
 [vhighlight_$counter]
 file = $track.track_file_style_conditional.track_input_bed_single
+line_width = $track.track_file_style_conditional.line_width
 color = $track.track_file_style_conditional.color
 alpha = $track.track_file_style_conditional.alpha
+border_color = $track.track_file_style_conditional.border_color
 type = vhighlight
   #end if
 
@@ -1185,11 +1191,29 @@
                 <when value="vlines_track_option">
                     <expand macro="track_input_bed_single_macro" />
                     <param name="line_width" type="float" value="0.5" label="width of lines"/>
+                    <param name="line_style" type="select" label="Line Style">
+                        <option value="dashed">Dashed</option>
+                        <option value="solid">Solid</option>
+                        <option value="dotted">Dotted</option>
+                        <option value="dashdot">Dashdot</option>
+                    </param>
+                    <param name="color" type="color" value="black" label="color of the vline"/>
+                    <param name="alpha" type="float" value="0.7" min="0" max="1" label="transparency (alpha) of the vline"/>
+                    <param name="zorder" type="select" label="Plot the vline above or behind other tracks">
+                        <option value="100">above</option>
+                        <option value="-100">behind</option>
+                    </param>
                 </when>
                 <when value="vhighlight_track_option">
                     <expand macro="track_input_bed_single_macro" />
                     <param name="color" type="color" value="yellow" label="color of the highlight"/>
                     <param name="alpha" type="float" value="0.5" min="0" max="1" label="transparency (alpha) of the highlight"/>
+                    <param name="line_width" type="float" min="0" value="0.5" label="width of the edge of the highlight" />
+                    <param name="border_color" type="color" value="yellow" label="color of the edge of the highlight"/>
+                    <param name="zorder" type="select" label="Plot the highlight above or behind other tracks">
+                        <option value="-100">behind</option>
+                        <option value="100">above</option>
+                    </param>
                 </when>
                 <when value="hlines_track_option">
                     <expand macro="plot_title" />
@@ -2169,6 +2193,19 @@
                 <conditional name="track_file_style_conditional">
                     <param name="track_file_style_selector" value="vlines_track_option" />
                     <param name="track_input_bed_single" value="dm3_subset_BDGP5.78_asbed4.bed.gz" ftype="bed" />
+                    <param name="line_width" value="2"/>
+                    <param name="zorder" value="100"/>
+                    <param name="color" value="red"/>
+                </conditional>
+            </repeat>
+            <repeat name="tracks">
+                <conditional name="track_file_style_conditional">
+                    <param name="track_file_style_selector" value="vlines_track_option" />
+                    <param name="track_input_bed_single" value="dm3_genes_end.bed" ftype="bed" />
+                    <param name="line_width" value="5"/>
+                    <param name="zorder" value="-100"/>
+                    <param name="color" value="blue"/>
+                    <param name="line_style" value="solid"/>
                 </conditional>
             </repeat>
             <param name="image_file_format" value="png" />
@@ -3336,16 +3373,13 @@
 Output
 ------
 
-**pyGenomeTracks** output is similar to a genome browser screen-shot that besides the usual genes, and score data (like bigwig or bedgraph files)
-may also contains Hi-C data. The plot is composed of tracks that need to be specified.
-Below is represented the 85 Mb to 110 Mb region from human chromosome 2 visualized using **pyGenomeTracks**.
-TADs were computed by HiCExplorer's ``hicFindTADs``. The additional tracks added correspond to:
-TAD-separation score (as reported by HiCExplorer's ``hicFindTADs``), chromatin states,
-principal component 1 (A/B compartment) computed using HiCExplorer's ``hicPCA``, ChIP-seq coverage for the H3K27ac mark, DNA methylation, and a gene track.
-Data are from mouse cardiac myocytes, published by `Nothjunge et al. (2017)`_.
+Here are two example plots with the different tracks you can use (on the right, you have the vlines and vhighlight which have been used):
 
-.. image:: $PATH_TO_IMAGES/pyGenomeTracks.png
-   :width: 70 %
+.. image:: static/images/demo.png
+   :width: 45 %
+.. image:: static/images/demo2.png
+   :width: 45 %
+
 
 _________________