--- a/macros.xml	Mon Oct 11 01:47:22 2021 +0000
+++ b/macros.xml	Mon Oct 11 16:40:51 2021 +0000
@@ -1,7 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.1.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
-dd
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
@@ -17,4 +16,164 @@
     <xml name="version_command">
         <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
     </xml>
+    <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="--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
+                             transcript_id1 and transcript_id2 in the given fusions file can be drawn.
+                             Selecting the isoform with the highest coverage usually produces nicer plots,
+                             in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint.
+                             However, the isoform with the highest coverage may not be the one that is involved in the fusion.
+                             Often, genomic rearrangements lead to non-canonical isoforms being transcribed.
+                             For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2,
+                             which reflect the actual isoforms involved in a fusion.
+\                            As a third option, the transcripts that are annotated as canonical can be drawn.
+                             Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.
+                        </help>
+                        <option value="coverage">coverage</option>
+                        <option value="provided">provided</option>
+                        <option value="canonical">canonical</option>
+                    </param>
+                    <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection">
+                        <help>The fusion of interest is drawn as a solid line in the circos plot.
+                              To give an impression of the overall degree of rearrangement,
+                              all other fusions are drawn as semi-transparent lines in the background.
+                              This option determines which other fusions should be included in the circos plot.
+                              Values specify the minimum confidence a fusion must have to be included.
+                              It usually makes no sense to include low-confidence fusions in circos plots,
+                              because they are abundant and unreliable, and would clutter up the circos plot.
+                              Default: medium
+                        </help>
+                        <option value="none">none - only the fusion of interest is drawn</option>
+                        <option value="low">low</option>
+                        <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
+                              Since introns are in most situations of no interest in the context of gene fusions,
+                              this switch can be used to shrink the size of introns to a fixed, negligible size.
+                              It makes sense to disable this feature, if breakpoints in introns are of importance.
+                              Default: TRUE
+                        </help>
+                        <option value="TRUE">True</option>
+                        <option value="FALSE">False</option>
+                    </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
+                              Protein tyrosine kinase and Protein kinase domain.
+                              In order to simplify the visualization, such domains can be merged into one,
+                              given that they overlap by the given fraction.
+                              The description of the larger domain is used.
+                              Default: 0.9
+                        </help>
+                    </param>
+                    <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels">
+                        <help>By default the number of an exon is printed inside each exon,
+                              which is taken from the attribute exon_number of the GTF annotation.
+                              When a gene has many exons, the boxes may be too narrow to contain the labels,
+                              resulting in unreadable exon labels. In these situations, i
+                              it may be better to turn off exon labels.
+                              Default: TRUE
+                        </help>
+                        <option value="TRUE">True</option>
+                        <option value="FALSE">False</option>
+                    </param>
+                    <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect">
+                        <help>Whether light and shadow should be rendered to give objects a 3D effect.
+                              Default: TRUE
+                        </help>
+                        <option value="TRUE">True</option>
+                        <option value="FALSE">False</option>
+                    </param>
+                    <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors">
+                        <help>By default, the script colorizes domains according to the colors
+                              specified in the file given in --annotation.
+                              This way, coloring of domains is consistent across all proteins.
+                              But since there are more distinct domains than colors,
+                              this can lead to different domains having the same color.
+                              If this option is set to TRUE, the colors are recomputed for each fusion separately.
+                              This ensures that the colors have the maximum distance for each individual fusion,
+                              but they are no longer consistent across different fusions.
+                              Default: FALSE
+                        </help>
+                        <option value="TRUE">True</option>
+                        <option value="FALSE">False</option>
+                    </param>
+                    <param argument="--color1" type="color" value="" optional="true"  label="Color of the 5' end of the fusion."/>
+                    <param argument="--color2" type="color" value="" optional="true"  label="Color of the 3' end of the fusion."/>
+                    <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"
+                           help="Default: 11.692"/>
+                    <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
+                           help="Default: 8.267"/>
+                    <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
+                           help="Default: 1.0"/>
+                </section>
+    </xml>
+    <token name="@DRAW_FUSIONS@">
+draw_fusions.R
+    --fusions='$fusions'
+    --alignments='Aligned.sortedByCoord.out.bam'
+    --annotation='$annotation'
+    --output=fusions.pdf
+    #if $visualization.cytobands
+    --cytobands='$visualization.cytobands'
+    #end if
+    #if $protein_domains
+    --proteinDomains='$protein_domains'
+    #end if
+    ## Visualization Options
+    #if $visualization.options.transcriptSelection
+        --transcriptSelection=$visualization.options.transcriptSelection
+    #end if
+    #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
+    #end if
+    #if $visualization.options.mergeDomainsOverlappingBy
+        --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
+    #end if
+    #if $visualization.options.printExonLabels
+        --printExonLabels=$visualization.options.printExonLabels
+    #end if
+    #if $visualization.options.render3dEffect
+        --render3dEffect=$visualization.options.render3dEffect
+    #end if
+    #if $visualization.options.optimizeDomainColors
+        --optimizeDomainColors=$visualization.options.optimizeDomainColors
+    #end if
+    #if $visualization.options.color1
+        --color1=$visualization.options.color1
+    #end if
+    #if $visualization.options.color2
+        --color2=$visualization.options.color2
+    #end if
+    #if $visualization.options.pdfWidth
+        --pdfWidth=$visualization.options.pdfWidth
+    #end if
+    #if $visualization.options.pdfHeight
+        --pdfHeight=$visualization.options.pdfHeight
+    #end if
+    #if $visualization.options.fontSize
+        --fontSize=$visualization.options.fontSize
+    #end if
+</token>
 </macros>