# HG changeset patch # User jjohnson # Date 1633916842 0 # Node ID 7253b367c082ba2bc5fab6b2ab95dae0c69562b6 # Parent 005b200c8841774966038cfd2bb1cf2e8c92bef0 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea" diff -r 005b200c8841 -r 7253b367c082 arriba.xml --- a/arriba.xml Sun Oct 10 13:00:45 2021 +0000 +++ b/arriba.xml Mon Oct 11 01:47:22 2021 +0000 @@ -70,10 +70,83 @@ #if $tags -t '$tags' #end if + #if str($wgs.use_wgs) == "yes" + -d '$wgs.wgs' + #if $wgs.max_genomic_breakpoint_distance + -D $wgs.max_genomic_breakpoint_distance + #end if + #end if -o fusions.tsv #if $output_fusions_discarded -O fusions.discarded.tsv #end if +## Arriba options + #if $options.gtf_features + -G $options.gtf_features + #end if + #if $options.strandedness + -s $options.strandedness + #end if + #if $options.genome_contigs + -i $options.genome_contigs + #end if + #if $options.viral_contigs + -v $options.viral_contigs + #end if + #if $options.max_evalue + -E $options.max_evalue + #end if + #if $options.min_supporting_reads + -S $options.min_supporting_reads + #end if + #if $options.max_mismappers + -m $options.max_mismappers + #end if + #if $options.max_homolog_identity + -L $options.max_homolog_identity + #end if + #if $options.homopolymer_length + -H $options.homopolymer_length + #end if + #if $options.read_through_distance + -R $options.read_through_distance + #end if + #if $options.min_anchor_length + -A $options.min_anchor_length + #end if + #if $options.many_spliced_events + -M $options.many_spliced_events + #end if + #if $options.max_kmer_content + -m $options.max_kmer_content + #end if + #if $options.max_mismatch_pvalue + -V $options.max_mismatch_pvalue + #end if + #if $options.fragment_length + -F $options.fragment_length + #end if + #if $options.max_reads + -U $options.max_reads + #end if + #if $options.quantile + -Q $options.quantile + #end if + #if $options.exonic_fraction + -e $options.exonic_fraction + #end if + #if $options.top_n + -T $options.top_n + #end if + #if $options.covered_fraction + -C $options.covered_fraction + #end if + #if $options.max_itd_length + -l $options.max_itd_length + #end if + $options.duplicate_marking + $options.fill_discarded_columns + $options.fill_the_gaps #if str($input_params.input_source) == "use_fastq" && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam && samtools index Aligned.sortedByCoord.out.bam @@ -85,16 +158,55 @@ && draw_fusions.R --fusions=fusions.tsv --alignments=Aligned.sortedByCoord.out.bam + --annotation='$gtf' --output=fusions.pdf - --annotation='$gtf' #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 #end if - ]]> @@ -139,7 +251,182 @@ - + + + + + + + + + + + +
+ + Commma or SPACE separated list, default: gene_name=gene_name gene_id=gene_id transcript_id=transcript_id feature_exon=exon feature_CDS=CDS + ^(gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=[^ ,]+([ ,](gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=[^ ,]+)?$ + + + When unstranded data is processed, the strand can sometimes be inferred from splice-patterns. But in unclear situations, stranded data helps resolve ambiguities. + + + + + + + Comma-/space-separated list of interesting contigs. + Fusions between genes on other contigs are ignored. Contigs can be specified with or without the prefix "chr". + Asterisks (*) are treated as wild-cards. + Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_* + + + + Comma-/space-separated list of viral contigs. + Asterisks (*) are treated as wild-cards. + Default: AC_* NC_* + + + + Arriba estimates the number of fusions with a given number of supporting + reads which one would expect to see by random chance. If the expected number + of fusions (e-value) is higher than this threshold, the fusion is + discarded by the 'relative_support' filter. Note: Increasing this + threshold can dramatically increase the number of false positives and may + increase the runtime of resource-intensive steps. Fractional values are possible. + Default: 0.300000 + + + + + discard all fusions with fewer than this many supporting reads (split reads and discordant mates combined). + Default: 2 + + + + When more than this fraction of supporting reads turns out to be mismappers, + the 'mismappers' filter discards the fusion. + Default: 0.800000 + + + + Genes with more than the given fraction of sequence identity are + considered homologs and removed by the 'homologs' filter. + Default: 0.300000 + + + + The 'homopolymer' filter removes breakpoints adjacent to homopolymers of the given length or more. + Default: 6 + + + + The 'read_through' filter removes read-through fusions + where the breakpoints are less than the given distance away from each other. + Default: 10000 + + + + Alignment artifacts are often characterized by split reads coming + from only one gene and no discordant mates. Moreover, the split + reads only align to a short stretch in one of the genes. The + 'short_anchor' filter removes these fusions. This parameter sets + the threshold in bp for what the filter considers short. + Default: 23 + + + + The 'many_spliced' filter recovers fusions between genes that + have at least this many spliced breakpoints. + Default: 4 + + + + The 'low_entropy' filter removes reads with repetitive 3-mers. If + the 3-mers make up more than the given fraction of the sequence, then + the read is discarded. + Default: 0.600000 + + + + + The 'mismatches' filter uses a binomial model to calculate a + p-value for observing a given number of mismatches in a read. + If the number of mismatches is too high, the read is discarded. + Default: 0.010000 + + + + + When paired-end data is given, the fragment length is estimated + automatically and this parameter has no effect. But when single-end + data is given, the mean fragment length should be specified to + effectively filter fusions that arise from hairpin structures. + Default: 200 + + + + Subsample fusions with more than the given number of supporting reads. This + improves performance without compromising sensitivity, as long as the + threshold is high. Counting of supporting reads beyond the threshold is + inaccurate, obviously. + Default: 300 + + + + Highly expressed genes are prone to produce artifacts during library preparation. + Genes with an expression above the given quantile are eligible for filtering by the 'in_vitro' filter. + Default: 0.998000 + + + + The breakpoints of false-positive predictions of intragenic events + are often both in exons. True predictions are more likely to have at + least one breakpoint in an intron, because introns are larger. + If the fraction of exonic sequence between two breakpoints is smaller than + the given fraction, the 'intragenic_exonic' filter discards the event. + Default: 0.330000 + + + + + Only report viral integration sites of the top N most highly expressed viral contigs. + Default: 5 + + + + Ignore virally associated events if the virus is not fully expressed, + i.e., less than the given fraction of the viral contig is transcribed. + Default: 0.150000 + + + + Note: Increasing this value beyond the default can impair performance and lead to many false positives. + Default: 100 + + + + Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a + preceding program using the BAM_FDUP flag. This makes sense when unique molecular + identifiers (UMI) are used. + + + + To reduce the runtime and file size, by default, the columns 'fusion_transcript', + 'peptide_sequence', and 'read_identifiers' are left empty in the file containing + discarded fusion candidates (see parameter -O). When this flag is set, this extra + information is reported in the discarded fusions file. + + + + If assembly of the fusion transcript sequence from the supporting reads is incomplete + (denoted as '...'), fill the gaps using the assembly sequence wherever possible. + + +
+ @@ -147,9 +434,115 @@ +
+ + 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 + + + + + + + + + +
+ + @@ -203,15 +596,16 @@