--- a/macros.xml	Fri May 26 07:54:18 2023 +0000
+++ b/macros.xml	Wed Oct 01 19:34:28 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.8</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">3.9</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">pygenometracks</requirement>
@@ -8,7 +8,11 @@
         </requirements>
         <version_command><![CDATA[@BINARY@ --version | tail -n 1 ]]></version_command>
     </xml>
-
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">pygenometracks</xref>
+        </xrefs>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1038/s41467-017-02525-w</citation>
@@ -40,9 +44,6 @@
     <xml name="track_input_bed_macro">
         <param name="track_input_bed" type="data" format="bed" label="Track file(s) bed format" multiple="True"/>
     </xml>
-    <xml name="track_input_bed_gtf_macro">
-        <param name="track_input_bed" type="data" format="bed,gtf" label="Track file(s) bed or gtf format" multiple="True"/>
-    </xml>
     <xml name="track_input_narrow_peak_macro">
         <param name="track_input_narrow_peak" type="data" format="encodepeak,bed" label="Track file(s) encodepeak or bed format" multiple="True"/>
     </xml>
@@ -207,24 +208,11 @@
         <param name="gene_rows" type="integer" value="" optional="True" label="Maximum number of gene rows" />
         <param name="max_labels" type="integer" value="60" label="Maximum number of gene labels to display" />
         <param name="line_width" type="float" value="0.5" label="width of lines" />
-        <section name ="gtf" title="When using gtf as input" expanded="False">
-            <param name="prefered_name" type="text" value="transcript_name" label="attribute to use as label"
-                help="Usually transcript_name or gene_name"/>
-            <conditional name="merge_transcripts">
-                <param name="merge_transcripts_select" type="select" label="Merge all transcripts of each gene in a single entry">
-                    <option value="false" selected="True">No</option>
-                    <option value="true">Yes</option>
-                </param>
-                <when value="true">
-                    <param name="merge_overlapping_exons" type="boolean" truevalue="true" falsevalue="false" checked="true"
-                        label="Merge overlapping exons" help="Usually it makes prettier plots" />
-                </when>
-                <when value="false" />
-            </conditional>
-        </section>
     </xml>
-    <xml name="utr_macro">
+    <xml name="height_utr_macro">
         <param name="height_utr" type="float" value="1" min="0" max="1" label="relative height of UTR regions compared to coding regions"/>
+    </xml>
+    <xml name="color_utr_macro">
         <conditional name="color_utr">
             <param name="color_utr_select" type="select" label="Define UTR color:">
                 <option value="manually" selected="True">manually</option>
@@ -238,6 +226,116 @@
             <when value="like" />
         </conditional>
     </xml>
+    <xml name="bed_arrow_macro">
+        <param name="arrow_interval" type="integer" value="2" min="0" label="interval between 2 arrows on exons"/>
+        <conditional name="color_arrow">
+            <param name="color_arrow_select" type="select" label="Define arrow color:">
+                <option value="manually" selected="True">manually</option>
+                <option value="bed_rgb">From the 9th field</option>
+            </param>
+            <when value="manually">
+                <param name="color" type="color" value="black" label="Color of arrows"/>
+            </when>
+            <when value="bed_rgb" />
+        </conditional>
+    </xml>
+    <xml name="bed_style_macro">
+        <conditional name="labels">
+            <param name="plot_labels" type="select" label="Plot labels">
+                <option value="true" selected="True">yes</option>
+                <option value="false">no</option>
+            </param>
+            <when value="true">
+                <param name="all_labels_inside" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                    label="Put all labels inside the plotted region"
+                    help="Put labels on the left of the region if the region ends after the plotted region."/>
+                <param name="labels_in_margin" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                    label="Allow to put labels in the right margin"
+                    help="Put labels in the margin if the region ends after the plotted region."/>
+                <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+                <param name="fontstyle" type="select" label="Fontstyle">
+                    <option value="normal" selected="True">normal</option>
+                    <option value="italic">italic</option>
+                    <option value="oblique">oblique</option>
+                </param>
+            </when>
+            <when value="false"/>
+        </conditional>
+        <conditional name="bed_style">
+            <param name="bed_style_select" type="select" label="Bed style">
+                <option value="flybase" selected="True">flybase (blocks with arrow at extremities)</option>
+                <option value="UCSC">UCSC (blocks with arrows in introns)</option>
+                <option value="tssarrow">tssarrow (blocks with arrow above at beginning)</option>
+                <option value="exonarrows">exonarrows (large blocks with arrows in exons and smaller blocks for introns)</option>
+            </param>
+            <when value="flybase">
+                <expand macro="border_color_bed_macro" />
+                <param name="arrowhead_included" type="boolean" truevalue="true" falsevalue="false" checked="false"
+                    label="Include the arrowhead in the bed interval:"
+                    help="When set to False, the arrow indicating the orientation of the interval is plotted outside of the interval."/>
+                <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
+                    label="Size of arrowhead relative to the plotted region"
+                    help="This size is also used to put space between the bed regions and their labels."/>
+                <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
+                    <expand macro="height_utr_macro" />
+                    <expand macro="color_utr_macro" />
+                    <expand macro="bed_advanced_macro" />
+                    <expand macro="backbone_color_bed_macro" />
+                </section>
+            </when>
+            <when value="UCSC">
+                <expand macro="border_color_bed_macro" />
+                <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
+                    <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
+                        label="Size of arrowhead relative to the plotted region"
+                        help="This size is also used to put space between the bed regions and their labels."/>
+                    <expand macro="bed_arrow_macro" />
+                    <expand macro="bed_advanced_macro" />
+                    <expand macro="backbone_color_bed_macro" />
+                </section>
+            </when>
+            <when value="tssarrow">
+                <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
+                    <param name="arrow_length" type="integer" optional="true" label="arrow length" help="the length of the arrow in bp (default is 4% of the plotted region)"/>
+                    <expand macro="height_utr_macro" />
+                    <expand macro="color_utr_macro" />
+                    <expand macro="bed_advanced_macro" />
+                    <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
+                        label="Size of arrowhead relative to the plotted region"
+                        help="This size is also used to put space between the bed regions and their labels."/>
+                </section>
+            </when>
+            <when value="exonarrows">
+                <expand macro="border_color_bed_macro" />
+                <section name="bed_advanced" title="Configure other bed parameters" expanded="False">
+                    <expand macro="bed_arrow_macro" />
+                    <param name="height_intron" type="float" value="0.5" min="0" max="1" label="relative height of introns compared to exons"/>
+                    <expand macro="color_utr_macro" />
+                    <expand macro="bed_advanced_macro" />
+                    <param name="arrowhead_fraction" type="float" value="0.004" min="0" max="1"
+                        label="Size of arrowhead relative to the plotted region"
+                        help="This size is also used to put space between the bed regions and their labels."/>
+                </section>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="delinv_labels">
+        <conditional name="labels">
+            <param name="plot_labels" type="select" label="Plot labels below">
+                <option value="true" selected="True">yes</option>
+                <option value="false">no</option>
+            </param>
+            <when value="true">
+                <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
+                <param name="fontstyle" type="select" label="Fontstyle">
+                    <option value="normal" selected="True">normal</option>
+                    <option value="italic">italic</option>
+                    <option value="oblique">oblique</option>
+                </param>
+            </when>
+            <when value="false"/>
+        </conditional>
+    </xml>
     <xml name="lines_macro">
         <param name="alpha" type="float" value="1" min="0" max="1" label="level of transparency (alpha)" help="1 is opaque and 0 is totally transparent"/>
         <param name="line_width" type="float" value="0.5" label="width of line(s)" optional="True"/>