arriba: arriba.xml annotate

annotate arriba.xml @ 4:77021ad5037d draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"

author	jjohnson
date	Sat, 09 Oct 2021 15:41:49 +0000
parents	2d32e6c86c48
children	005b200c8841

rev	line source
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	1 <tool id="arriba" name="Arriba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	2 <description>detect gene fusions from STAR aligned RNA-Seq data</description>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	3 <macros>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	4 <import>macros.xml</import>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	5 </macros>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	6 <expand macro="requirements" />
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	7 <expand macro="version_command" />
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	9 #if str($input_params.input_source) == "use_fastq"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	10 #if $input_params.left_fq.is_of_type("fastq.gz"):
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	11 #set read1 = 'input_1.fastq.gz'
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	12 #else:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	13 #set read1 = 'input_1.fastq'
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	14 #end if
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	15 ln -f -s '${input_params.left_fq}' ${read1} &&
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	16 #if $input_params.right_fq.is_of_type("fastq.gz"):
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	17 #set read2 = 'input_2.fastq.gz'
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	18 #else:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	19 #set read2 = 'input_2.fastq'
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	20 #end if
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	21 ln -f -s '${input_params.right_fq}' ${read2} &&
2 7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	22 #if str($input_params.index.index_source) == "history"
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	23 #set $star_index_dir = $input_params.index.star_index.extra_files_path
2 7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	24 #end if
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	25 STAR
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	26 --runThreadN \${GALAXY_SLOTS:-1}
2 7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	27 --genomeDir $star_index_dir
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	28 --genomeLoad NoSharedMemory
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	29 --readFilesIn $read1 $read2
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	30 --readFilesCommand zcat
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	31 --outStd BAM_Unsorted
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	32 --outSAMtype BAM Unsorted
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	33 --outSAMunmapped Within
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	34 --outBAMcompression 0
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	35 --outFilterMultimapNmax 50
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	36 --peOverlapNbasesMin 10
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	37 --alignSplicedMateMapLminOverLmate 0.5
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	38 --alignSJstitchMismatchNmax 5 -1 5 5
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	39 --chimSegmentMin 10
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	40 --chimOutType WithinBAM HardClip
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	41 --chimJunctionOverhangMin 10
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	42 --chimScoreDropMax 30
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	43 --chimScoreJunctionNonGTAG 0
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	44 --chimScoreSeparation 1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	45 --chimSegmentReadGapMax 3
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	46 --chimMultimapNmax 50
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	47 \| tee Aligned.out.bam \|
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	48 arriba
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	49 -x '/dev/stdin'
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	50 #else
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	51 arriba
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	52 -x '$input_params.input'
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	53 #if $input_params.chimeric
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	54 -c '$input_params.chimeric'
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	55 #end if
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	56 #end if
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	57 -a '$genome_assembly'
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	58 -g '$gtf'
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	59 #if $blacklist
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	60 -b '$blacklist'
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	61 #else
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	62 -f 'blacklist'
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	63 #end if
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	64 #if $protein_domains
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	65 -p '$protein_domains'
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	66 #end if
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	67 #if $known_fusions
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	68 -k '$known_fusions'
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	69 #end if
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	70 #if $tags
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	71 -t '$tags'
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	72 #end if
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	73 -o fusions.tsv
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	74 -O fusions.discarded.tsv
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	75 #if str($input_params.input_source) == "use_fastq"
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	76 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	77 && samtools index Aligned.sortedByCoord.out.bam
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	78 #elif str($visualization.do_viz) == "yes"
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	79 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	80 && samtools index Aligned.sortedByCoord.out.bam
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	81 #end if
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	82 #if str($visualization.do_viz) == "yes"
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	83 && draw_fusions.R
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	84 --fusions=fusions.tsv
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	85 --alignments=Aligned.sortedByCoord.out.bam
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	86 --output=fusions.pdf
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	87 --annotation='$gtf'
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	88 #if $visualization.cytobands
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	89 --cytobands='$visualization.cytobands'
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	90 #end if
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	91 #if '$protein_domains'
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	92 --proteinDomains='$protein_domains'
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	93 #end if
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	94 #end if
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	95
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	96 ]]></command>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	97 <inputs>
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	98 <conditional name="input_params">
2 7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	99 <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR">
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	100 <option value="use_star">Use output from earlier STAR</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	101 <option value="use_fastq">Let Arriba control running STAR</option>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	102 </param>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	103 <when value="use_star">
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	104 <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"/>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	105 <param name="chimeric" argument="-c" type="data" format="sam,bam,cram" optional="true" label="STAR Chimeric.out.sam">
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	106 <help><![CDATA[ only required, if STAR was run with the parameter '--chimOutType SeparateSAMold' ]]></help>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	107 </param>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	108 </when>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	109 <when value="use_fastq">
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	110 <param name="left_fq"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	111 type="data"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	112 format="fastqsanger,fastqsanger.gz"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	113 argument="--left_fq"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	114 label="left.fq file"/>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	115 <param name="right_fq"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	116 type="data"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	117 format="fastqsanger,fastqsanger.gz"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	118 argument="--right_fq"
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	119 label="right.fq file"/>
2 7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	120 <conditional name="index">
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	121 <param name="index_source" type="select" label="Arriba STAR index source">
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	122 <option value="history">Arriba STAR index from your history</option>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	123 </param>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	124 <when value="history">
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	125 <param name="star_index" argument="--genomeDir" type="data" format="txt" label="Arriba STAR index"
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	126 help="generated by: Arriba Reference"/>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	127 </when>
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	128 </conditional>
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	129 </when>
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	130 </conditional>
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	131 <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	132 <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	133 <param name="blacklist" argument="-b" type="data" format="tabular" optional="true" label="File containing blacklisted ranges."/>
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	134 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	135 <param name="known_fusions" argument="-k" type="data" format="tabular" optional="true" label="File containing known fusions">
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	136 <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	137 </param>
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	138 <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	139 help="This can be the known fusions if that input has a third column with a name"/>
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	140 <conditional name="visualization">
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	141 <param name="do_viz" type="select" label="Generate visualization">
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	142 <option value="yes">Yes</option>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	143 <option value="no">no</option>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	144 </param>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	145 <when value="yes">
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	146 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	147 </when>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	148 <when value="no"/>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	149 </conditional>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	150
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	151 </inputs>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	152 <outputs>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	153 <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	154 <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"/>
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	155 <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	156 <filter>input_params['input_source'] == "use_fastq"</filter>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	157 </data>
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	158 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
3 2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	159 <filter>visualization['do_viz'] == "yes"</filter>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96" jjohnson parents: 2 diff changeset	160 </data>
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	161 </outputs>
4 77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	162 <tests>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	163 <!-- Test 1 - From exisitng BAM -->
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	164 <test>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	165 <conditional name="input_params">
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	166 <param name="input_source" value="use_star"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	167 <param name="input" ftype="sam" value="Aligned.out.sam"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	168 </conditional>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	169 <param name="genome_assembly" ftype="fasta" value="genome.fasta"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	170 <param name="gtf" ftype="gtf" value="genome.gtf"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	171 <conditional name="visualization">
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	172 <param name="do_viz" value="no"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	173 </conditional>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	174 <output name="fusions">
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	175 <assert_contents>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	176 <has_text_matching expression="BCR\tABL1"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	177 </assert_contents>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	178 </output>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	179 </test>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" jjohnson parents: 3 diff changeset	180 </tests>
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	181 <help><![CDATA[
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	182 Arriba
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	183
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	184
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	185 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	186 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	187
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	188
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	189 INPUTS_
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	190
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	191
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	192 - Alignments
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	193
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	194 Arriba takes the main output file of STAR (Aligned.out.bam) as input (parameter -x). If STAR was run with the parameter --chimOutType WithinBAM, then this file contains all the information needed by Arriba to find fusions. When STAR was run with the parameter --chimOutType SeparateSAMold, the main output file lacks chimeric alignments. Instead, STAR writes them to a separate output file named Chimeric.out.sam. In this case, the file needs to be passed to Arriba via the parameter -c in addition to the main output file Aligned.out.bam.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	195
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	196 Arriba extracts three types of reads from the alignment file(s):
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	197
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	198 * Split-reads, i.e., reads composed of segments which map in a non-linear way. STAR stores such reads as supplementary alignments.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	199 * Discordant mates, i.e., paired-end reads which originate from the same fragment but which align in a non-linear way.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	200 * Alignments which cross the boundaries of annotated genes, because these alignments might arise from focal deletions. In RNA-Seq data deletions of up to several hundred kb are hard to distinguish from splicing. They are represented identically as gapped alignments, because the sizes of many introns are in fact of this order of magnitude. STAR applies a rather arbitrary measure to decide whether a gapped alignment arises from splicing or from a genomic deletion: The parameter --alignIntronMax determines what gap size is still assumed to be a splicing event and introns are used to represent these gaps. Only gaps larger than this limit are classified as potential evidence for genomic deletions and are stored as chimeric alignments. Most STAR-based fusion detection tools only consider chimeric alignments as evidence for gene fusions and are blind to focal deletions, hence. As a workaround, these tools recommend reducing the value of the parameter --alignIntronMax. But this impairs the quality of alignment, because it reduces the scope that STAR searches to find a spliced alignment. To avoid compromising the quality of alignment for the sake of fusion detection, the only solution would be to run STAR twice - once with settings optimized for regular alignment and once for fusion detection. This would double the runtime. In contrast, Arriba does not require to reduce the maximum intron size. It employs a more sensible criterion to distinguish splicing from deletions: Arriba considers all those reads as potential evidence for deletions that span the boundary of annotated genes.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	201
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	202 The alignment files can be in SAM, BAM, and CRAM format. They need not be sorted for Arriba to accept them, but doing so comes with benefits: Often, this reduces the file size. And more importantly, the supporting reads of a fusion can be inspected visually using a genome browser like IGV, which typically requires BAM files to be sorted by coordinate.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	203
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	204 Single-end and paired-end data and even mixtures are supported. Arriba automatically determines the data type on a read-by-read basis using the flag BAM_FPAIRED.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	205
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	206
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	207 - Assembly
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	208
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	209 Arriba takes the assembly as input (parameter -a) to find mismatches between the chimeric reads and the reference genome, as well as to find alignment artifacts and homologous genes.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	210
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	211 The script download_references.sh can be used to download the assembly. The available assemblies are listed when the script is run without parameters. The user is not restricted to these assemblies, however. Any assembly can be used as long as its coordinates are compatible with one of the supported assemblies (hg19/hs37d5/GRCh37 or hg38/GRCh38 or mm10/GRCm38).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	212
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	213 The assembly must be provided in FastA format and may be gzip-compressed. An index with the file extension .fai must exist only if CRAM files are processed.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	214
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	215 - Annotation
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	216
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	217 The gene annotation (parameter -g) is used for multiple purposes:
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	218
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	219 annotation of breakpoints with genes
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	220 increased sensitivity for breakpoints at splice-sites
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	221 calculation of transcriptomic distances
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	222 determining the putative orientation of fused genes (i.e., 5' and 3' end)
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	223 GENCODE annotation is recommended over RefSeq annotation, because the former has a more comprehensive annotation of transcripts and splice-sites, which boosts the sensitivity. The file must be provided in GTF format and may be gzip-compressed. It does not need to be sorted.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	224
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	225 The script download_references.sh can be used to download the annotation. The available annotation files are listed when the script is run without parameters. The user is not restricted to these annotation files, however. Any annotation can be used as long as its coordinates are compatible with one of the supported assemblies (hg19/hs37d5/GRCh37 or hg38/GRCh38 or mm10/GRCm38).
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	226
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	227
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	228 - Blacklist
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	229
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	230 It is strongly advised to run Arriba with a blacklist (parameter -b). Otherwise, the false positive rate increases by an order of magnitude. For this reason, using Arriba with assemblies or organisms which are not officially supported is not recommended. At the moment, the supported assemblies are: hg19/hs37d5/GRCh37, hg38/GRCh38, and mm10/GRCm38 (as well as any other assemblies that have compatible coordinates). The blacklists are contained in the release tarballs of Arriba.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	231
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	232 The blacklist removes recurrent alignment artifacts and transcripts which are present in healthy tissue. This helps eliminate frequently observed transcripts, such as read-through fusions between neighboring genes, circular RNAs and other non-canonically spliced transcripts. It was trained on RNA-Seq samples from the Human Protein Atlas, the Illumina Human BodyMap2 , the ENCODE project , the Roadmap Epigenomics project, and the NCT MASTER cohort, a heterogeneous cohort of cancer samples, from which highly recurrent artifacts were identified.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	233
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	234 Blacklists for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/blacklist_*.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	235
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	236 The blacklist is a tab-separated file with two columns and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions between which events are ignored. A region can be:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	237 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). If CONTIG ends on an asterisk (*), the contig with the closest matching name is chosen.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	238 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	239 * the name of a gene given in the provided annotation.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	240
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	241 In addition, special keywords are allowed for the second column:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	242 * any: Discard all events if one of the breakpoints matches the given region.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	243 * split_read_donor: Discard fusions only supported by split reads, if all of them have their anchor in the gene given in the first column. This filter is useful for highly mutable loci, which frequently trigger clipped alignments, such as the immunoglobulin loci or the T-cell receptor loci.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	244 * split_read_acceptor: Discard events only supported by split reads, if all of them have their clipped segment in the given region.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	245 * split_read_any: Discard events only supported by split reads, regardless of where the anchor is.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	246 * discordant_mates: Discard fusions, if they are only supported by discordant mates (no split reads).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	247 * low_support: Discard events, which have few supporting reads relative to expression (as determined by the filter relative_support), even if there is other evidence that the fusion might be a true positive, nonetheless. This keyword effectively prevents recovery of speculative events by filters such as spliced or many_spliced.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	248 * filter_spliced: This keyword prevents the filter spliced from being applied to a given region. It is triggered under the same circumstances as the keyword low_support, but additionally requires that the breakpoints be at splice-sites for the event to be discarded. Some breakpoints produce recurrent artifacts, but the second breakpoint is always a different one, such that the pair of breakpoints is not recurrent and cannot be blacklisted. Often, such breakpoints are at splice-sites and the filter spliced tends to recover them. This keyword prevents the filter from doing so.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	249 * not_both_spliced: This keyword discards events, unless both breakpoints are at splice-sites. This is a strict blacklist criterion, which makes sense to apply to genes which are prone to produce artifacts, because they are highly expressed, for example hemoglobins, collagens, or ribosomal genes.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	250 * read_through: This keyword discards events, if they could arise from read-through transcription, i.e., the supporting reads are oriented like a deletion and are at most 400 kb apart.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	251
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	252
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	253 - Known fusions
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	254
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	255 Arriba can be instructed to be particularly sensitive towards events between certain gene pairs by supplying a list of gene pairs (parameter -k). A number of filters are not applied to these gene pairs. This is useful to improve the detection rate of expected or highly relevant events, such as recurrent fusions. Occassionally, this leads to false positive calls. But if high sensitivity is more important than specificity, this might be acceptable. Events which would be discarded by a filter and were recovered due to being listed in the known fusions list are usually assigned a low confidence.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	256
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	257 Known fusions files for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/known_fusions_*.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	258
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	259 The file has two columns separated by a tab and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions to which very sensitive filtering thresholds are applied. A region can be:
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	260
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	261 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). If CONTIG ends on an asterisk (*), the contig with the closest matching name is chosen.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	262 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	263 * the name of a gene given in the provided annotation.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	264
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	265 The order of the given regions is important. The region given in the first column is assumed to denote the 5' end of the fusion and the region in the second column to be the 3' end. If Arriba cannot determine with confidence which gene constitutes the 5' and which the 3' end of a fusion prediction, then the order is ignored and the prediction is rescued in both cases.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	266
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	267
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	268 - Tags
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	269
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	270 Arriba can be supplied with a list of user-defined tags using the parameter -t. Whenever a fusion prediction matches the selection criteria for a tag, the column tags is populated with the respective tag. This feature is useful to annotate known oncogenic fusions, for example.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	271
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	272 The known fusions file shipped with the download package of Arriba can be used for both known fusions and tags. It is constructed in a way that it can be passed as arguments to the parameters -k and -t alike. The former only uses the first two columns, the latter uses all three columns. If a user wants to separate filtering of known fusions and tagging of interesting fusions, different files may be used, however.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	273
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	274 The file has three columns separated by a tab and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions to be annotated. The first two columns specify the regions to be annotated; the third column the tag that is used for annotation. Some special characters in the tag are replaced with underscores (_) in Arriba's output file. A region can be:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	275
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	276 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	277 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	278 * the name of a gene given in the provided annotation.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	279
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	280 The order of the given regions is important. The region given in the first column is assumed to denote the 5' end of the fusion and the region in the second column to be the 3' end.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	281
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	282 - Protein domains
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	283
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	284 Protein domain annotation can be passed to Arriba via the parameter -p. The column retained_protein_domains of Arriba's output file is then populated accordingly.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	285
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	286 Protein domain annotation files for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/protein_domains_*.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	287
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	288 The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	289 * Name=PROTEIN_DOMAIN_NAME;
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	290 * gene_id=GENE_ID;
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	291 * gene_name=GENE_NAME
2 7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c" jjohnson parents: 1 diff changeset	292
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	293 The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	294
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	295 - Structural variant calls from WGS
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	296
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	297 If whole-genome sequencing (WGS) data is available, the sensitivity and specificity of Arriba can be improved by passing a list of structural variants detected from WGS to Arriba via the parameter -d. This has the following effects:
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	298
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	299 Certain filters are overruled or run with extra sensitive settings, when an event is confirmed by WGS data.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	300 To reduce the false positive rate, Arriba does not report low-confidence events unless they can be matched with a structural variant found in the WGS data.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	301 Both of these behaviors can be disabled by disabling the filters genomic_support and no_genomic_support, respectively. Providing Arriba with a list of structural variant calls then does not influence the calls, but it still has the benefit of filling the columns closest_genomic_breakpoint1 and closest_genomic_breakpoint2 with the breakpoints of the structural variant which is closest to a fusion. If the structural variant calls were obtained from whole-exome sequencing (WES) data rather than WGS data, the filter no_genomic_support should be disabled, since WES has poor coverage in most regions of the genome, such that many structural variants are missed.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	302
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	303 Two file formats are accepted: a simple four-column format and the standard Variant Call Format (VCF). The format is detected automatically.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	304
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	305 * In case of the simple format, the file must contain four columns separated by tabs. The first two columns contain the breakpoints of the structural variants in the format CONTIG:POSITION. The last two columns contain the orientation of the breakpoints. The accepted values are:
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	306
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	307 + downstream or +: the fusion partner is fused downstream of the breakpoint, i.e., at a coordinate higher than the breakpoint
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	308 + upstream or -: the fusion partner is fused at a coordinate lower than the breakpoint
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	309
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	310 Example:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	311
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	312 ::
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	313
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	314 =========== =========== =========== ===========
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	315 5-prime 3-prime orientation orientation
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	316 =========== =========== =========== ===========
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	317 1:54420491 6:9248349 + -
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	318 20:46703288 20:46734546 - +
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	319 17:61499820 20:45133874 + +
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	320 3:190967119 7:77868317 - -
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	321 =========== =========== =========== ===========
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	322
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	323
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	324 * In case of the Variant Call Format, the file must comply with the VCF specification for structural variants. In particular, Arriba requires that the SVTYPE field be present in the INFO column and specify one of the four values BND, DEL, DUP, INV. In addition, for all SVTYPEs other than BND, the END field must be present and specify the second breakpoint of the structural variant. Structural variants with single breakends are silently ignored.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	325
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	326 Arriba checks if the orientation of the structural variant matches that of a fusion detected in the RNA-Seq data. If, for example, Arriba predicts the 5' end of a gene to be retained in a fusion, then a structural variant is expected to confirm this, or else the variant is not considered to be related.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	327
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	328 NOTE: Arriba was designed for alignments from RNA-Seq data. It should not be run on WGS data directly. Many assumptions made by Arriba about the data (statistical models, blacklist, etc.) only apply to RNA-Seq data and are not valid for DNA-Seq data. For such data, a structural variant calling algorithm should be used and the results should be passed to Arriba.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	329
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	330
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	331 OUTPUTS_
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	332
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	333 - fusions.tsv
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	334
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	335 The file fusions.tsv (as specified by the parameter -o) contains fusions which pass all of Arriba's filters. It should be highly enriched for true predictions. The predictions are listed from highest to lowest confidence. The following paragraphs describe the columns in detail:
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	336
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	337 * gene1 and gene2 : gene1 contains the gene which makes up the 5' end of the transcript and gene2 the gene which makes up the 3' end. The order is predicted on the basis of the strands that the supporting reads map to, how the reads are oriented, and splice patterns. Both columns may contain the same gene, if the event is intragenic. If a breakpoint is in an intergenic region, Arriba lists the closest genes upstream and downstream from the breakpoint, separated by a comma. The numbers in parentheses after the closest genes state the distance to the genes. If no genes are annotated for a contig (e.g., for viral genomes), the column contains a dot (.).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	338
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	339 * strand1(gene/fusion) and strand2(gene/fusion) : Each of these columns contains two values seperated by a slash. The strand before the slash reflects the strand of the gene according to the gene annotation supplied to Arriba via the parameter -g. If the breakpoint is in an intergenic region, the value is .. The value after the slash reflects the strand that is transcribed. This does not necessarily match the strand of the gene, namely when the sense strand of a gene serves as the template for transcription. Occassionally, the strand that is transcribed cannot be predicted reliably. In this case, Arriba indicates the lack of information as a dot (.). Arriba uses splice-patterns of the alignments to assign a read to the appropriate originating gene. If a strand-specific library was used, Arriba also evaluates the strandedness in ambiguous situations, for example, when none of the supporting reads overlaps a splice-site.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	340
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	341 * breakpoint1 and breakpoint2 : The columns contain the coordinates of the breakpoints in gene1 and gene2, respectively. If an event is not supported by any split reads but only by discordant mates, the coordinates given here are those of the discordant mates which are closest to the true but unknown breakpoint.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	342
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	343 * site1 and site2 : These columns add information about the location of the breakpoints. Possible values are: 5' UTR, 3' UTR, UTR (overlapping with a 5' UTR as well as a 3' UTR), CDS (coding sequence), exon, intron, and intergenic. The keyword exon is used for non-coding genes or for ambiguous situations where the breakpoint overlaps with both a coding exon and a UTR. If the breakpoint coincides with an exon boundary, the additional keyword splice-site is appended.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	344
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	345 * type : Based on the orientation of the supporting reads and the coordinates of breakpoints, the type of event can be inferred. Possible values are: translocation (between different chromosomes), duplication, inversion, and deletion. If genes are fused head-to-head or tail-to-tail, this is indicated as 5'-5' or 3'-3' respectively. Genes fused in such an orientation cannot yield a chimeric protein, since one of the genes is transcribed from the wrong strand. This type of event is equivalent to the truncation of the genes. The following types of events are flagged with an extra keyword, because they are frequent types of false positives and/or it is not clear if they are somatic or germline variants: Deletions with a size in the range of introns (<400kb) are flagged as read-through, because there is a high chance that the fusion arises from read-through transcription rather than an underlying genomic deletion. Intragenic duplications with both breakpoints at splice-sites are flagged as non-canonical-splicing, because the supporting reads might originate from circular RNAs, which are very abundant even in normal tissue, but manifest as duplications in RNA-Seq data. Internal tandem duplications are flagged as ITD. It is not always clear whether the ITDs observable in RNA-Seq data are somatic or germline variants, because ITDs are abundant in the germline and germline variants cannot be filtered effectively due to lack of a normal control.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	346
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	347 * split_reads1 and split_reads2 : The number of supporting split fragments with an anchor in gene1 or gene2, respectively, is given in these columns. The gene to which the longer segment of the split read aligns is defined as the anchor.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	348
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	349 * discordant_mates : This column contains the number of pairs (fragments) of discordant mates (a.k.a. spanning reads or bridge reads) supporting the fusion.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	350
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	351 * coverage1 and coverage2 : These two columns show the coverage near breakpoint1 and breakpoint2, respectively. The coverage is calculated as the number of fragments near the breakpoint on the side of the breakpoint that is retained in the fusion transcript. Note that the coverage calculation counts all fragments (even duplicates), whereas the columns split_reads1, split_reads2, and discordant_mates only count non-discarded reads. Fragments discarded due to being duplicates or other types of artifacts can be found in the column filters.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	352
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	353 * confidence : Each prediction is assigned one of the confidences low, medium, or high. Several characteristics are taken into account, including: the number of supporting reads, the balance of split reads and discordant mates, the distance between the breakpoints, the type of event, whether the breakpoints are intragenic or not, and whether there are other events which corroborate the prediction, e.g. multiple isoforms or balanced translocations. See section Interpretation of results for further advice on judging the credibility of predictions.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	354
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	355 * reading_frame : This column states whether the gene at the 3' end of the fusion is fused in-frame or out-of-frame. The value stop-codon indicates that there is a stop codon prior to the fusion junction, such that the 3' end is not translated, even if the reading frame is preserved across the junction. The prediction of the reading frame builds on the prediction of the peptide sequence. A dot (.) indicates that the peptide sequence cannot be predicted, for example, because the transcript sequence could not be determined or because the breakpoint of the 5' gene does not overlap a coding region.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	356
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	357 * tags : When a user-defined list of tags is provided via the parameter -t, this column is populated with the provided tag whenever a fusion matches the coordinates specified for the respective tag. When multiple tags match, they are separated by a comma.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	358
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	359 * retained_protein_domains : If Arriba is provided with protein domain annotation using the parameter -p, then this column is populated with protein domains retained in the fusion. Multiple protein domains are separated by a comma. Redundant protein domains are only listed once. After every domain the fraction that is retained is stated as a percentage value in parentheses. The protein domains of the 5' and 3' genes are separated by a pipe symbol (\|).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	360
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	361 * closest_genomic_breakpoint1 and closest_genomic_breakpoint2 : When a matched whole-genome sequencing sample is available, one can feed structural variant calls obtained therefrom into Arriba (see parameter -d). Arriba then considers this information during fusion calling, which improves the overall accuracy. These two columns contain the coordinates of the genomic breakpoints which are closest to the transcriptomic breakpoints given in the columns breakpoint1 and breakpoint2. The values in parentheses are the distances between transcriptomic and genomic breakpoints.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	362
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	363 * gene_id1 and gene_id2 : These two columns state the identifiers of the fused genes as given in the gene_id attribute in the GTF file.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	364
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	365 * transcript_id1 and transcript_id2 : For both fused genes, Arriba determines the best matching isoform that is transcribed as part of the fusion. The isoform is selected by how well its annotated exons match the splice pattern of the supporting reads of a fusion.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	366
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	367 * direction1 and direction2 : These columns indicate the orientation of the fusion. A value of downstream means that the partner is fused downstream of the breakpoint, i.e. at a coordinate higher than the breakpoint. A value of upstream means the partner is fused at a coordinate lower than the breakpoint. When the prediction of the strands or of the 5' gene fails, this information gives insight into which parts of the fused genes are retained in the fusion.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	368
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	369 * filters : This column lists the filters which removed one or more of the supporting reads. The section Internal algorithm describes all filters in detail. The number of filtered reads is given in parentheses after the name of the filter. The total number of supporting reads can be obtained by summing up the reads given in the columns split_reads1, split_reads2, discordant_mates, and filters. If a filter discarded the event as a whole (all reads), the number of filtered reads is not stated.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	370
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	371 * fusion_transcript : This column contains the fusion transcript sequence. The sequence is assembled from the supporting reads of the most highly expressed transcript. It represents the transcript isoform that is most likely expressed according to the splice patterns of the supporting reads. The column contains a dot (.), when the sequence could not be predicted. This is the case when the strands or the 5' end of the transcript could not be predicted reliably. The breakpoint is represented as a pipe symbol (\|). When non-template bases are inserted between the fused genes, these bases are represented as lowercase letters between two pipes. Reference mismatches (SNPs or SNVs) are indicated as lowercase letters, insertions as bases between brackets ([ and ]), deleted bases as one or more dashes (-), introns as three underscores (___), and ambiguous positions, such as positions with diverse reference mismatches, are represented as ?. Missing information due to insufficient coverage is denoted as an ellipsis (...). If the switch -I is used, then an attempt is made to fill missing information with the assembly sequence. A sequence stretch that was taken from the assembly sequence rather than the supporting reads is wrapped in parentheses (( and )). In addition, when -I is used, the sequence is trimmed to the boundaries of the fused transcripts. The coordinate of the fusion breakpoint relative to the start of the transcript can thus easily be inferred by counting the bases from the beginning of the fusion transcript to the breakpoint character (\|). In case the full sequence could be constructed from the combined information of supporting reads and assembly sequence, the start of the fusion transcript is marked by a caret sign (^) and the end by a dollar sign ($). If the full sequence could not be constructed, these signs are missing.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	372
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	373 * peptide_sequence : This column contains the fusion peptide sequence. The sequence is translated from the fusion transcript given in the column fusion_transcript and determines the reading frame of the fused genes according to the transcript isoforms given in the columns transcript_id1 and transcript_id2. Translation starts at the start of the assembled fusion transcript or when the start codon is encountered in the 5' gene. Translation ends when either the end of the assembled fusion transcript is reached or when a stop codon is encountered. If the fusion transcript contains an ellipsis (...), the sequence beyond the ellipsis is trimmed before translation, because the reading frame cannot be determined reliably. The column contains a dot (.), when the transcript sequence could not be predicted or when the precise breakpoints are unknown due to lack of split reads or when the fusion transcript does not overlap any coding exons in the 5' gene or when no start codon could be found in the 5' gene or when there is a stop codon prior to the fusion junction (in which case the column reading_frame contains the value stop-codon). The breakpoint is represented as a pipe symbol (\|). If a codon spans the breakpoint, the amino acid is placed on the side of the breakpoint where two of the three bases reside. Codons resulting from non-template bases are flanked by two pipes. Amino acids are written as lowercase characters in the following situations: non-silent SNVs/SNPs, insertions, frameshifts, codons spanning the breakpoint, non-coding regions (introns/intergenic regions/UTRs), and non-template bases. Codons which cannot be translated to amino acids, such as those having invalid characters, are represented as ?.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	374
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	375 * read_identifiers : This column contains the names of the supporting reads separated by commas.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	376
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	377 - fusions.discarded.tsv
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	378
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	379 The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv.
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	380
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	381
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	382
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	383
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	384
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	385 Code repository: https://github.com/suhrig/arriba
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	386 Get help/report bugs: https://github.com/suhrig/arriba/issues
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	387 User manual: https://arriba.readthedocs.io/
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	388 Please cite: https://doi.org/10.1101/gr.257246.119
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	389
1 9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	390
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	391 .. _Arriba: https://arriba.readthedocs.io/en/latest/
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	392 .. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685" jjohnson parents: 0 diff changeset	393 .. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/
0 5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	394
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	395 ]]></help>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	396 <expand macro="citations" />
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2" jjohnson parents: diff changeset	397 </tool>

Mercurial > repos > jjohnson > arriba

annotate arriba.xml @ 4:77021ad5037d draft