--- a/macros.xml	Fri Feb 11 19:09:19 2022 +0000
+++ b/macros.xml	Mon Jun 13 12:10:34 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.2.1</token>
+    <token name="@TOOL_VERSION@">2.3.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
@@ -49,6 +49,7 @@
     <xml name="visualization_options">
                 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
                 <section name="options" expanded="false" title="Draw Fusion Options">
+                    <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>
                     <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
                         <help>By default the transcript isoform with the highest coverage is drawn.
                              Alternatively, the transcript isoform that is provided in the columns
@@ -81,14 +82,6 @@
                         <option value="medium">medium</option>
                         <option value="high">high</option>
                     </param>
-                    <param argument="--showIntergenicVicinity" type="integer" value="" min="0" optional="true" label="Intergenic Vicinity">
-                        <help>This option only applies to intergenic breakpoints.
-                              If it is set to a value greater than 0, then the script draws the genes
-                              which are no more than the given distance away from an intergenic breakpoint.
-                              Note that this option is incompatible with squishIntrons.
-                              Default: 0
-                        </help>
-                    </param>
                     <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
                         <help>Exons usually make up only a small fraction of a gene.
                               They may be hard to see in the plot. i
@@ -100,7 +93,24 @@
                         <option value="TRUE">True</option>
                         <option value="FALSE">False</option>
                     </param>
-
+                    <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity">
+                        <help>This option only applies to intergenic breakpoints.
+                              If it is set to a value greater than 0, then the script draws the genes
+                              which are no more than the given distance away from an intergenic breakpoint.
+                              The keywords closestGene and closestProteinCodingGene instruct the script 
+                              to dynamically determine the distance to the next (protein-coding) gene for each breakpoint. 
+                              Alternatively, instead of specifying a single distance 
+                              that is applied upstream and downstream of both breakpoints alike, 
+                              more fine-grained control over the region to be shown is possible by specifying four comma-separated values. 
+                              The first two values determine the region to the left and to the right of breakpoint 1; 
+                              the third and fourth values determine the region to the left and to the right of breakpoint 2. 
+                              Note that this option is incompatible with squishIntrons.
+                              Default: 0
+                        </help>
+                        <option value="closestGene">closestGene</option>
+                        <option value="closestProteinCodingGene">closestProteinCodingGene</option>
+                        <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$</validator>
+                    </param>
                     <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
                         <help>Occasionally, domains are annotated redundantly.
                               For example, tyrosine kinase domains are frequently annotated as
@@ -151,6 +161,67 @@
                            help="Default: 8.267"/>
                     <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
                            help="Default: 1.0"/>
+                    <param argument="--fontFamily" type="text" value="" optional="true" label="Font to use for all labels in the plots.">
+                        <help>Default: Helvetica
+                        </help>
+                        <option value="serif">serif</option>
+                        <option value="sans">sans</option>
+                        <option value="mono">mono</option>
+                        <option value="AvantGarde">AvantGarde</option>
+                        <option value="Bookman">Bookman</option>
+                        <option value="Courier">Courier</option>
+                        <option value="Helvetica">Helvetica</option>
+                        <option value="Helvetica-Narrow">Helvetica-Narrow</option>
+                        <option value="NewCenturySchoolbook">NewCenturySchoolbook</option>
+                        <option value="Palatino">Palatino</option>
+                        <option value="Times">Times</option>
+                        <option value="URWGothic">URWGothic</option>
+                        <option value="URWBookman">URWBookman</option>
+                        <option value="NimbusMon">NimbusMon</option>
+                        <option value="NimbusSan">NimbusSan</option>
+                        <option value="URWHelvetica">URWHelvetica</option>
+                        <option value="NimbusSanCond">NimbusSanCond</option>
+                        <option value="CenturySch">CenturySch</option>
+                        <option value="URWPalladio">URWPalladio</option>
+                        <option value="NimbusRom">NimbusRom</option>
+                        <option value="URWTimes">URWTimes</option>
+                        <option value="ArialMT">ArialMT</option>
+                        <option value="Japan1">Japan1</option>
+                        <option value="Japan1HeiMin">Japan1HeiMin</option>
+                        <option value="Japan1GothicBBB">Japan1GothicBBB</option>
+                        <option value="Japan1Ryumin">Japan1Ryumin</option>
+                        <option value="Korea1">Korea1</option>
+                        <option value="Korea1deb">Korea1deb</option>
+                        <option value="CNS1">CNS1</option>
+                        <option value="GB1">GB1</option>
+                    </param>
+                    <param argument="--fixedScale" type="integer" value="" min="0" optional="true" label="Apply a fixed scale to all fusions">
+                        <help>By default, transcripts are scaled automatically to fill the entire page. 
+                              This parameter enforces a fixed scale to be applied to all fusions, 
+                              which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable. 
+                              A common use case is the visualization of a gene that is found to be fused to multiple partners. 
+                              By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage 
+                              in a single plot one above the other with matching scales. 
+                              Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn, 
+                              or else dynamic scaling is applied, because display errors would occur otherwise. 
+                              The default value is 0, which means that no fixed scale should be used 
+                              and that the scale should be adapted dynamically for each fusion. Default: 0
+                        </help>
+                    </param>
+                    <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot">
+                        <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes. 
+                              The plots can be cropped at a fixed level by passing a non-zero value to this parameter. 
+                              When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level. 
+                              When two comma-separated values are given, the cutoffs can be specified independently for the two plots. 
+                              A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage) 
+                              and that the coverage plots of both genes should be on the same scale. This is the default behavior. 
+                              A value of 0,0 also indicates that no cropping should be applied, 
+                              but the coverage plots of the two genes have different scales: 
+                              each one is scaled individually to the peak coverage of the respective gene. 
+                              Default: 0
+                        </help>
+                        <validator type="regex" message="">^\d+(,\d+)?$</validator>
+                    </param>
                 </section>
     </xml>
     <token name="@DRAW_FUSIONS@">
@@ -172,18 +243,24 @@
     #if $visualization.options.minConfidenceForCircosPlot
         --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
     #end if
-    #if $visualization.options.showIntergenicVicinity
-        --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
-    #end if
     #if $visualization.options.squishIntrons
         --squishIntrons=$visualization.options.squishIntrons
+        #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity
+            --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
+        #end if
     #end if
     #if $visualization.options.mergeDomainsOverlappingBy
         --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
     #end if
+    #if $visualization.options.sampleName
+        --sampleName=$visualization.options.sampleName
+    #end if
     #if $visualization.options.printExonLabels
         --printExonLabels=$visualization.options.printExonLabels
     #end if
+    #if $visualization.options.coverageRange
+        --coverageRange="$visualization.options.coverageRange"
+    #end if
     #if $visualization.options.render3dEffect
         --render3dEffect=$visualization.options.render3dEffect
     #end if
@@ -202,6 +279,10 @@
     #if $visualization.options.pdfHeight
         --pdfHeight=$visualization.options.pdfHeight
     #end if
+    # fontFamily
+    #if $visualization.options.fontFamily
+        --fontFamily=$visualization.options.fontFamily
+    #end if
     #if $visualization.options.fontSize
         --fontSize=$visualization.options.fontSize
     #end if