--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jul 27 11:25:43 2022 +0000
@@ -0,0 +1,311 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.3.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/gr.257246.119</citation>
+            <yield />
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
+    </xml>
+    <xml name="genome_source" token_assembly_optional="false" >
+        <conditional name="genome">
+            <param name="genome_source" type="select" label="Genome assembly fasta (that was used for STAR alignment)">
+                <option value="history">From your history</option>
+                <option value="cached">Use built-in Genome reference</option>
+            </param>
+            <when value="history">
+                <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/>
+            </when>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
+                    <options from_data_table="all_fasta">
+                        <validator type="no_options" message="No reference genomes are available" />
+                    </options>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="gtf_source" token_assembly_optional="false" >
+        <conditional name="genome_gtf">
+            <param name="gtf_source" type="select" label="Genome GTF annotation source">
+                <option value="history">From your history</option>
+                <!-- <option value="cached">Use built-in Gtf annotation</option> -->
+            </param>
+            <when value="history">
+                <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/>
+            </when>
+        </conditional>
+    </xml>
+
+    <token name="@GENOME_SOURCE@"><![CDATA[
+#if str($genome.genome_source) == "history"
+    #if $genome.assembly
+        #set $genome_assembly = 'genome.fa'
+        ln -sf '$genome.assembly' $genome_assembly &&
+    #end if
+#elif str($genome.genome_source) == "cached"
+    #set $genome_assembly = $genome.ref_file.fields.fasta
+#end if
+    ]]></token>
+    <token name="@GTF_SOURCE@"><![CDATA[
+#if str($genome_gtf.gtf_source) == "history"
+    #if $genome_gtf.annotation.is_of_type('gtf.gz')
+        #set $genome_annotation = 'genome.gtf.gz'
+    #else
+        #set $genome_annotation = 'genome.gtf'
+    #end if
+    ln -sf '$genome_gtf.annotation' $genome_annotation &&
+#end if
+    ]]></token>
+
+    <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
+                             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="--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="--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
+                              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"/>
+                    <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+)?$</validator>
+                    </param>
+                </section>
+    </xml>
+    <token name="@DRAW_FUSIONS@">
+draw_fusions.R
+    --fusions='$fusions'
+    --alignments='Aligned.sortedByCoord.out.bam'
+    --annotation='$genome_gtf.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 $visualization.options.squishIntrons
+        --squishIntrons=$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
+    #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 str($visualization.options.pdfWidth)
+        --pdfWidth=$visualization.options.pdfWidth
+    #end if
+    #if str($visualization.options.pdfHeight)
+        --pdfHeight=$visualization.options.pdfHeight
+    #end if
+    # fontFamily
+    #if $visualization.options.fontFamily
+        --fontFamily=$visualization.options.fontFamily
+    #end if
+    #if str($visualization.options.fontSize)
+        --fontSize=$visualization.options.fontSize
+    #end if
+</token>
+</macros>