# HG changeset patch
# User jjohnson
# Date 1633970451 0
# Node ID 25d207f7ff836d0c07ce6b3886c4ec4c608ecac4
# Parent 7253b367c082ba2bc5fab6b2ab95dae0c69562b6
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
diff -r 7253b367c082 -r 25d207f7ff83 arriba.xml
--- a/arriba.xml Mon Oct 11 01:47:22 2021 +0000
+++ b/arriba.xml Mon Oct 11 16:40:51 2021 +0000
@@ -55,7 +55,7 @@
#end if
#end if
-a '$genome_assembly'
- -g '$gtf'
+ -g '$annotation'
#if $blacklist
-b '$blacklist'
#else
@@ -155,57 +155,8 @@
&& samtools index Aligned.sortedByCoord.out.bam
#end if
#if str($visualization.do_viz) == "yes"
-&& draw_fusions.R
- --fusions=fusions.tsv
- --alignments=Aligned.sortedByCoord.out.bam
- --annotation='$gtf'
- --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
+#set $fusions = 'fusions.tsv'
+&& @DRAW_FUSIONS@
#end if
]]>
@@ -243,7 +194,7 @@
-
+
@@ -433,120 +384,15 @@
-
-
-
- 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.
-
-
-
-
-
-
- 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
-
-
-
-
-
-
-
- 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
-
-
-
- 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
-
-
-
-
-
-
- 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
-
-
-
- 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
-
-
-
-
-
- Whether light and shadow should be rendered to give objects a 3D effect.
- Default: TRUE
-
-
-
-
-
- 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
-
-
-
-
-
-
-
-
-
-
-
+
-
-
+
+
output_fusions_discarded == "yes"
@@ -564,13 +410,13 @@
-
+
-