arriba: arriba.xml annotate

annotate arriba.xml @ 5:5e03d09d5fdc draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0

author	iuc
date	Fri, 04 Apr 2025 10:37:49 +0000
parents	98163e8ed458
children

rev	line source
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	1 <tool id="arriba" name="Arriba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	2 <description>detect gene fusions from STAR aligned RNA-Seq data</description>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	3 <macros>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	4 <import>macros.xml</import>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	5 <xml name="fusion_actions">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	6 <actions>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	7 <action name="comment_lines" type="metadata" default="1" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	8 <action name="column_names" type="metadata" default="gene1,gene2,strand1(gene/fusion),strand2(gene/fusion),breakpoint1,breakpoint2,site1,site2,type,split_reads1,split_reads2,discordant_mates,coverage1,coverage2,confidence,reading_frame,tags,retained_protein_domains,closest_genomic_breakpoint1,closest_genomic_breakpoint2,gene_id1,gene_id2,transcript_id1,transcript_id2,direction1,direction2,filters,fusion_transcript,peptide_sequence,read_identifiers" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	9 </actions>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	10 </xml>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	11 <token name="@VIRAL_CONTIG@">([AN]C_([*]\|\d+))</token>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	12 <token name="@GENOME_CONTIG@">((chr)?(\d\|\d\d\|X\|Y\|M(t)?))</token>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	13 </macros>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	14 <expand macro="requirements" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	15 <expand macro="version_command" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	16 <command detect_errors="exit_code"><![CDATA[
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	17 @GENOME_SOURCE@
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	18 @GTF_SOURCE@
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	19 #set $filter_list = []
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	20 #if $options.filters
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	21 #set $filter_list = $options.filters.split(',')
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	22 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	23 #if $blacklist
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	24 #if $blacklist.is_of_type('tabular.gz')
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	25 #set $blacklist_file = 'blacklist.tsv.gz'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	26 ln -sf '$blacklist' $blacklist_file &&
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	27 #else
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	28 #set $blacklist_file = $blacklist
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	29 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	30 #else
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	31 #if 'blacklist' not in $filter_list
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	32 #silent $filter_list.append('blacklist')
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	33 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	34 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	35 #set $filters = ','.join($filter_list)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	36 #if $known_fusions
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	37 #if $known_fusions.is_of_type('tabular.gz')
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	38 #set $known_fusions_file = 'known_fusions.tsv.gz'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	39 ln -sf '$known_fusions' $known_fusions_file &&
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	40 #else
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	41 #set $known_fusions_file = $known_fusions
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	42 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	43 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	44 #if $tags
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	45 #if $tags.is_of_type('tabular.gz')
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	46 #set $tags_file = 'tags.tsv.gz'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	47 ln -sf '$tags' $tags_file &&
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	48 #else
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	49 #set $tags_file = $tags
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	50 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	51 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	52 arriba
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	53 -x '$input'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	54 #if $chimeric
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	55 -c '$chimeric'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	56 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	57 -a '$genome_assembly'
1 1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	58 -g 'genome.gtf'
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	59 #if $blacklist
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	60 -b '$blacklist_file'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	61 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	62 #if $filters
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	63 -f '$filters'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	64 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	65 #if $protein_domains
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	66 -p '$protein_domains'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	67 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	68 #if $known_fusions
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	69 -k '$known_fusions_file'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	70 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	71 #if $tags
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	72 -t '$tags_file'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	73 #end if
1 1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	74 #if str($wgs_cond.use_wgs) == "yes"
1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	75 -d '$wgs_cond.wgs'
2 eb3200075443 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 0856836a21e5cf745547dfcf0b9b98eb106e4952 iuc parents: 1 diff changeset	76 #if str($wgs_cond.max_genomic_breakpoint_distance)
1 1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	77 -D $wgs_cond.max_genomic_breakpoint_distance
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	78 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	79 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	80 -o fusions.tsv
1 1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	81 #if $output_fusions_discarded
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	82 -O fusions.discarded.tsv
1 1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	83 #end if
1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	84 ## Arriba options
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	85 #if $options.gtf_features
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	86 -G '$options.gtf_features'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	87 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	88 #if $options.strandedness
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	89 -s $options.strandedness
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	90 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	91 #if $options.genome_contigs
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	92 -i '$options.genome_contigs'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	93 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	94 #if $options.viral_contigs
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	95 -v '$options.viral_contigs'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	96 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	97 #if str($options.max_evalue)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	98 -E $options.max_evalue
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	99 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	100 #if str($options.min_supporting_reads)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	101 -S $options.min_supporting_reads
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	102 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	103 #if str($options.max_mismappers)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	104 -m $options.max_mismappers
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	105 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	106 #if str($options.max_homolog_identity)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	107 -L $options.max_homolog_identity
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	108 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	109 #if str($options.homopolymer_length)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	110 -H $options.homopolymer_length
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	111 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	112 #if str($options.read_through_distance)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	113 -R $options.read_through_distance
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	114 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	115 #if str($options.min_anchor_length)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	116 -A $options.min_anchor_length
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	117 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	118 #if str($options.many_spliced_events)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	119 -M $options.many_spliced_events
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	120 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	121 #if str($options.max_kmer_content)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	122 -K $options.max_kmer_content
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	123 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	124 #if str($options.max_mismatch_pvalue)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	125 -V $options.max_mismatch_pvalue
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	126 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	127 #if str($options.fragment_length)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	128 -F $options.fragment_length
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	129 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	130 #if str($options.max_reads)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	131 -U $options.max_reads
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	132 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	133 #if $options.quantile
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	134 -Q $options.quantile
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	135 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	136 #if str($options.exonic_fraction)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	137 -e $options.exonic_fraction
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	138 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	139 #if str($options.top_n)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	140 -T $options.top_n
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	141 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	142 #if str($options.covered_fraction)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	143 -C $options.covered_fraction
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	144 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	145 #if str($options.max_itd_length)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	146 -l $options.max_itd_length
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	147 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	148 #if str($options.min_itd_allele_fraction)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	149 -z $options.min_itd_allele_fraction
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	150 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	151 #if str($options.min_itd_supporting_reads)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	152 -Z $options.min_itd_supporting_reads
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	153 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	154 $options.duplicate_marking
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	155 $options.fill_discarded_columns
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	156 $options.fill_the_gaps
3 2eca65b822be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 7943aa76786271a466aa1b0e2c8fac3f32176863 iuc parents: 2 diff changeset	157 #if $output_fusion_bams or str($visualization.do_viz) == "yes"
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	158 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	159 && samtools index Aligned.sortedByCoord.out.bam
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	160 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	161 #if $output_fusions_vcf
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	162 && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	163 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	164 #if $output_fusion_bams
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	165 && mkdir fusion_bams
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	166 && extract_fusion-supporting_alignments.sh fusions.tsv Aligned.sortedByCoord.out.bam 'fusion_bams/fusion'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	167 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	168 #if str($visualization.do_viz) == "yes"
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	169 #set $fusions = 'fusions.tsv'
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	170 && @DRAW_FUSIONS@
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	171 #end if
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	172 ]]></command>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	173 <inputs>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	174 <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	175 <help><![CDATA[ recommended STAR options: --chimSegmentMin 10 --chimOutType WithinBAM ]]></help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	176 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	177 <param name="chimeric" argument="-c" type="data" format="sam,bam,cram" optional="true" label="STAR Chimeric.out.sam">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	178 <help><![CDATA[ only required, if STAR was run with the parameter '--chimOutType SeparateSAMold' ]]></help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	179 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	180 <expand macro="genome_source" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	181 <expand macro="gtf_source" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	182 <param name="blacklist" argument="-b" type="data" format="tabular,tabular.gz" optional="true" label="File containing blacklisted ranges."/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	183 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	184 <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz" optional="true" label="File containing known fusions">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	185 <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	186 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	187 <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	188 help="This can be the known fusions if that input has a third column with a name"/>
1 1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	189 <conditional name="wgs_cond">
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	190 <param name="use_wgs" type="select" label="Use whole-genome sequencing data">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	191 <option value="no">no</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	192 <option value="yes">Yes</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	193 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	194 <when value="yes">
1 1e5f6ea1762a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	195 <param name="wgs" argument="-d" type="data" format="tabular,vcf" label="whole-genome sequencing structural variant data"
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	196 help="These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence."/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	197 <param name="max_genomic_breakpoint_distance" argument="-D" type="integer" value="100000" min="0" label="Max genomic breakpoint distance"
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	198 help="determines how far a genomic breakpoint may be away from a transcriptomic breakpoint to consider it as a related event."/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	199 </when>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	200 <when value="no"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	201 </conditional>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	202 <section name="options" expanded="false" title="Arriba Options">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	203 <param name="gtf_features" argument="-G" type="text" value="" optional="true" label="Names of features in the GTF annotation file">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	204 <help>Commma or SPACE separated list, default: gene_name=gene_name\|gene_id gene_id=gene_id transcript_id=transcript_id feature_exon=exon feature_CDS=CDS</help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	205 <validator type="regex" message="">^(gene_name\|gene_id\|transcript_id\|feature_exon\|feature_CDS)=\w+(\|\w+)?([ ,](gene_name\|gene_id\|transcript_id\|feature_exon\|feature_CDS)=\w+(\|\w+)?)*$</validator>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	206 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	207 <param name="strandedness" argument="-s" type="select" optional="true" label="Whether a strand-specific protocol was used for library preparation">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	208 <help>When unstranded data is processed, the strand can sometimes be inferred from splice-patterns. But in unclear situations, stranded data helps resolve ambiguities.</help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	209 <option value="auto">auto</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	210 <option value="yes">yes</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	211 <option value="no">no</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	212 <option value="reverse">reverse</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	213 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	214 <param name="genome_contigs" argument="-i" type="text" value="" optional="true" label="Comma/space-separated list of interesting contigs">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	215 <help>Comma-/space-separated list of interesting contigs.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	216 Fusions between genes on other contigs are ignored. Contigs can be specified with or without the prefix "chr".
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	217 Asterisks (*) are treated as wild-cards.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	218 Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	219 </help>
4 98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685 iuc parents: 3 diff changeset	220 <validator type="regex" message="not a valid contig name">^((@GENOME_CONTIG@\|@VIRAL_CONTIG@)([,\s]\s(@GENOME_CONTIG@\|@VIRAL_CONTIG@)))$</validator>
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	221 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	222 <param name="viral_contigs" argument="-v" type="text" value="" optional="true" label="Comma/space-separated list of viral contigs">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	223 <help>Comma-/space-separated list of viral contigs for reporting of viral integration sites.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	224 Asterisks (*) are treated as wild-cards.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	225 Default: AC_* NC_*
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	226 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	227 <validator type="regex" message="not a valid contig name">^(@VIRAL_CONTIG@([,\s]\s@VIRAL_CONTIG@))*$</validator>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	228 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	229 <param name="filters" argument="-f" type="select" optional="true" multiple="true" label="Disable filters">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	230 <help>By default all filters are enabled.</help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	231 <option value="top_expressed_viral_contigs">top_expressed_viral_contigs</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	232 <option value="viral_contigs">viral_contigs</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	233 <option value="low_coverage_viral_contigs">low_coverage_viral_contigs</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	234 <option value="uninteresting_contigs">uninteresting_contigs</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	235 <option value="no_genomic_support">no_genomic_support</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	236 <option value="short_anchor">short_anchor</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	237 <option value="select_best">select_best</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	238 <option value="many_spliced">many_spliced</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	239 <option value="long_gap">long_gap</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	240 <option value="merge_adjacent">merge_adjacent</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	241 <option value="hairpin">hairpin</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	242 <option value="small_insert_size">small_insert_size</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	243 <option value="same_gene">same_gene</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	244 <option value="genomic_support">genomic_support</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	245 <option value="read_through">read_through</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	246 <option value="no_coverage">no_coverage</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	247 <option value="mismatches">mismatches</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	248 <option value="homopolymer">homopolymer</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	249 <option value="low_entropy">low_entropy</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	250 <option value="multimappers">multimappers</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	251 <option value="inconsistently_clipped">inconsistently_clipped</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	252 <option value="duplicates">duplicates</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	253 <option value="homologs">homologs</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	254 <option value="blacklist">blacklist</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	255 <option value="mismappers">mismappers</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	256 <option value="spliced">spliced</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	257 <option value="relative_support">relative_support</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	258 <option value="min_support">min_support</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	259 <option value="known_fusions">known_fusions</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	260 <option value="end_to_end">end_to_end</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	261 <option value="non_coding_neighbors">non_coding_neighbors</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	262 <option value="isoforms">isoforms</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	263 <option value="intronic">intronic</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	264 <option value="in_vitro">in_vitro</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	265 <option value="intragenic_exonic">intragenic_exonic</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	266 <option value="internal_tandem_duplication">internal_tandem_duplication</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	267 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	268
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	269 <param name="max_evalue" argument="-E" type="float" value="" min="0" optional="true" label="Max e-value threshold">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	270 <help>Arriba estimates the number of fusions with a given number of supporting
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	271 reads which one would expect to see by random chance. If the expected number
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	272 of fusions (e-value) is higher than this threshold, the fusion is
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	273 discarded by the 'relative_support' filter. Note: Increasing this
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	274 threshold can dramatically increase the number of false positives and may
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	275 increase the runtime of resource-intensive steps. Fractional values are possible.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	276 Default: 0.300000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	277 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	278 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	279
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	280 <param name="min_supporting_reads" argument="-S" type="integer" value="" min="1" optional="true" label="Min supporting reads">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	281 <help>discard all fusions with fewer than this many supporting reads (split reads and discordant mates combined).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	282 Default: 2
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	283 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	284 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	285 <param name="max_mismappers" argument="-m" type="float" value="" min="0." max="1.0" optional="true" label="Max mismappers threshold">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	286 <help>When more than this fraction of supporting reads turns out to be mismappers,
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	287 the 'mismappers' filter discards the fusion.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	288 Default: 0.800000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	289 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	290 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	291 <param name="max_homolog_identity" argument="-L" type="float" value="" min="0." max="1.0" optional="true" label="Max homologs identity threshold">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	292 <help>Genes with more than the given fraction of sequence identity are
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	293 considered homologs and removed by the 'homologs' filter.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	294 Default: 0.300000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	295 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	296 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	297 <param name="homopolymer_length" argument="-H" type="integer" value="" min="1" optional="true" label="Homopolymer length">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	298 <help>The 'homopolymer' filter removes breakpoints adjacent to homopolymers of the given length or more.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	299 Default: 6
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	300 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	301 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	302 <param name="read_through_distance" argument="-R" type="integer" value="" min="1" optional="true" label="Read-through distance">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	303 <help>The 'read_through' filter removes read-through fusions
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	304 where the breakpoints are less than the given distance away from each other.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	305 Default: 10000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	306 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	307 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	308 <param name="min_anchor_length" argument="-A" type="integer" value="" min="1" optional="true" label="Min anchor length">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	309 <help>Alignment artifacts are often characterized by split reads coming
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	310 from only one gene and no discordant mates. Moreover, the split
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	311 reads only align to a short stretch in one of the genes. The
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	312 'short_anchor' filter removes these fusions. This parameter sets
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	313 the threshold in bp for what the filter considers short.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	314 Default: 23
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	315 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	316 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	317 <param name="many_spliced_events" argument="-M" type="integer" value="" min="1" optional="true" label="Many spliced events">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	318 <help>The 'many_spliced' filter recovers fusions between genes that
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	319 have at least this many spliced breakpoints.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	320 Default: 4
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	321 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	322 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	323 <param name="max_kmer_content" argument="-K" type="float" value="" min="0." max="1.0" optional="true" label="Max kmer content">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	324 <help>The 'low_entropy' filter removes reads with repetitive 3-mers. If
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	325 the 3-mers make up more than the given fraction of the sequence, then
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	326 the read is discarded.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	327 Default: 0.600000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	328 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	329 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	330
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	331 <param name="max_mismatch_pvalue" argument="-V" type="float" value="" min="0." max="1." optional="true" label="Max mismatchrpvalue threahold">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	332 <help>The 'mismatches' filter uses a binomial model to calculate a
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	333 p-value for observing a given number of mismatches in a read.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	334 If the number of mismatches is too high, the read is discarded.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	335 Default: 0.010000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	336 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	337 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	338
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	339 <param name="fragment_length" argument="-F" type="integer" value="" min="1" optional="true" label="Single-end fragment length">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	340 <help>When paired-end data is given, the fragment length is estimated
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	341 automatically and this parameter has no effect. But when single-end
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	342 data is given, the mean fragment length should be specified to
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	343 effectively filter fusions that arise from hairpin structures.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	344 Default: 200
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	345 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	346 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	347 <param name="max_reads" argument="-U" type="integer" value="" min="1" optional="true" label="Max reads">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	348 <help>Subsample fusions with more than the given number of supporting reads. This
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	349 improves performance without compromising sensitivity, as long as the
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	350 threshold is high. Counting of supporting reads beyond the threshold is
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	351 inaccurate, obviously.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	352 Default: 300
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	353 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	354 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	355 <param name="quantile" argument="-Q" type="float" value="" min="0." max="1.0" optional="true" label="Quantile">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	356 <help>Highly expressed genes are prone to produce artifacts during library preparation.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	357 Genes with an expression above the given quantile are eligible for filtering by the 'in_vitro' filter.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	358 Default: 0.998000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	359 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	360 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	361 <param name="exonic_fraction" argument="-e" type="float" value="" min="0." max="1.0" optional="true" label="Exonic fraction">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	362 <help>The breakpoints of false-positive predictions of intragenic events
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	363 are often both in exons. True predictions are more likely to have at
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	364 least one breakpoint in an intron, because introns are larger.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	365 If the fraction of exonic sequence between two breakpoints is smaller than
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	366 the given fraction, the 'intragenic_exonic' filter discards the event.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	367 Default: 0.330000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	368 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	369 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	370
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	371 <param name="top_n" argument="-T" type="integer" value="" min="1" optional="true" label="top N viral contigs">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	372 <help>Only report viral integration sites of the top N most highly expressed viral contigs.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	373 Default: 5
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	374 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	375 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	376 <param name="covered_fraction" argument="-C" type="float" value="" min="0." max="1.0" optional="true" label="Covered fraction">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	377 <help>Ignore virally associated events if the virus is not fully expressed,
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	378 i.e., less than the given fraction of the viral contig is transcribed.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	379 Default: 0.050000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	380 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	381 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	382 <param name="max_itd_length" argument="-l" type="integer" value="" min="1" optional="true" label="Maximum length of internal tandem duplications">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	383 <help>Note: Increasing this value beyond the default can impair performance and lead to many false positives.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	384 Default: 100
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	385 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	386 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	387 <param name="min_itd_allele_fraction" argument="-z" type="float" value="" min="0." max="1.0" optional="true" label="Required fraction of supporting reads to report an internal tandem duplication">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	388 <help> Default: 0.070000
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	389 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	390 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	391 <param name="min_itd_supporting_reads" argument="-Z" type="integer" value="" min="1" optional="true" label="Required number of supporting reads to report an internal tandem duplication">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	392 <help> Default: 10
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	393 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	394 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	395 <param name="duplicate_marking" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Use aligners duplicate marking">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	396 <help>Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	397 preceding program using the BAM_FDUP flag. This makes sense when unique molecular
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	398 identifiers (UMI) are used.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	399 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	400 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	401 <param name="fill_discarded_columns" argument="-X" type="boolean" truevalue="-X" falsevalue="" checked="false" label="Fill all fusion.discarded.tsv columns">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	402 <help>To reduce the runtime and file size, by default, the columns 'fusion_transcript',
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	403 'peptide_sequence', and 'read_identifiers' are left empty in the file containing
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	404 discarded fusion candidates (see parameter -O). When this flag is set, this extra
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	405 information is reported in the discarded fusions file.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	406 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	407 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	408 <param name="fill_the_gaps" argument="-I" type="boolean" truevalue="-I" falsevalue="" checked="false" label="Fill fusion transcript gaps from the assembly">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	409 <help>If assembly of the fusion transcript sequence from the supporting reads is incomplete
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	410 (denoted as '...'), fill the gaps using the assembly sequence wherever possible.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	411 </help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	412 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	413 </section>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	414 <param name="output_fusions_discarded" argument="-O" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.discarded.tsv"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	415 <param name="output_fusions_vcf" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.vcf"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	416 <param name="output_fusion_bams" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output fusion BAMs"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	417 <conditional name="visualization">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	418 <param name="do_viz" type="select" label="Generate visualization">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	419 <option value="yes">Yes</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	420 <option value="no">no</option>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	421 </param>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	422 <when value="yes">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	423 <expand macro="visualization_options" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	424 </when>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	425 <when value="no"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	426 </conditional>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	427 </inputs>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	428 <outputs>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	429 <data name="fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	430 <expand macro="fusion_actions" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	431 </data>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	432
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	433 <data name="discarded_fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	434 <filter> output_fusions_discarded == True</filter>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	435 <expand macro="fusion_actions" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	436 </data>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	437 <data name="fusions_vcf" format="vcf" label="${tool.name} on ${on_string}: fusions.vcf" from_work_dir="fusions.vcf">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	438 <filter> output_fusions_vcf == True</filter>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	439 </data>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	440 <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	441 <discover_datasets pattern="(?P<name>fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	442 <filter>output_fusion_bams == True</filter>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	443 </collection>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	444 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	445 <filter>visualization['do_viz'] == "yes"</filter>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	446 </data>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	447 </outputs>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	448 <tests>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	449 <!-- Test 1 - From exisitng BAM -->
3 2eca65b822be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 7943aa76786271a466aa1b0e2c8fac3f32176863 iuc parents: 2 diff changeset	450 <test expect_num_outputs="3">
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	451 <param name="input" ftype="sam" value="Aligned.out.sam"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	452 <conditional name="genome">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	453 <param name="genome_source" value="history"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	454 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	455 </conditional>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	456 <conditional name="genome_gtf">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	457 <param name="gtf_source" value="history"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	458 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	459 </conditional>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	460 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	461 <conditional name="visualization">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	462 <param name="do_viz" value="no"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	463 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	464 </conditional>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	465 <output name="fusions_tsv">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	466 <assert_contents>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	467 <has_text_matching expression="BCR\tABL1"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	468 </assert_contents>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	469 </output>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	470 </test>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	471 <!-- Test 2 - From exisitng BAM with protein_domains and visualization -->
3 2eca65b822be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 7943aa76786271a466aa1b0e2c8fac3f32176863 iuc parents: 2 diff changeset	472 <test expect_num_outputs="4">
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	473 <param name="input" ftype="sam" value="Aligned.out.sam"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	474 <conditional name="genome">
4 98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685 iuc parents: 3 diff changeset	475 <param name="genome_source" value="cached"/>
98163e8ed458 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685 iuc parents: 3 diff changeset	476 <param name="ref_file" value="genome_id"/>
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	477 </conditional>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	478 <conditional name="genome_gtf">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	479 <param name="gtf_source" value="history"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	480 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	481 </conditional>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	482 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	483 <conditional name="visualization">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	484 <param name="do_viz" value="yes"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	485 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	486 </conditional>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	487 <output name="fusions_tsv">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	488 <assert_contents>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	489 <has_text_matching expression="BCR\tABL1"/>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	490 </assert_contents>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	491 </output>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	492 <output name="fusions_pdf">
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	493 <assert_contents>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	494 <has_size value= "64000" delta="5000" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	495 </assert_contents>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	496 </output>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	497 </test>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	498
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	499 </tests>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	500 <help><![CDATA[
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	501 Arriba
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	502
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	503
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	504 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	505 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	506
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	507
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	508 INPUTS
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	509
5 5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	510 See: https://github.com/suhrig/arriba/wiki/04-Input-files
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	511
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	512 - Alignments
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	513
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	514 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	515
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	516 STAR index create recommended parameter value:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	517
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	518 * --sjdbOverhang 250
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	519
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	520
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	521 STAR recommended parameter values ::
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	522
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	523 * --outSAMunmapped Within
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	524 * --outFilterMultimapNmax 50
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	525 * --peOverlapNbasesMin 10
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	526 * --alignSplicedMateMapLminOverLmate 0.5
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	527 * --alignSJstitchMismatchNmax 5 -1 5 5
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	528 * --chimSegmentMin 10
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	529 * --chimOutType WithinBAM HardClip
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	530 * --chimJunctionOverhangMin 10
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	531 * --chimScoreDropMax 30
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	532 * --chimScoreJunctionNonGTAG 0
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	533 * --chimScoreSeparation 1
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	534 * --chimSegmentReadGapMax 3
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	535 * --chimMultimapNmax 50
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	536
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	537
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	538 Arriba extracts three types of reads from the alignment file(s):
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	539
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	540 * Split-reads, i.e., reads composed of segments which map in a non-linear way. STAR stores such reads as supplementary alignments.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	541 * Discordant mates, i.e., paired-end reads which originate from the same fragment but which align in a non-linear way.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	542 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	543
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	544 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	545
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	546 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	547
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	548
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	549 - Assembly
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	550
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	551 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	552
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	553 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).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	554
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	555 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	556
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	557 - Annotation
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	558
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	559 The gene annotation (parameter -g) is used for multiple purposes:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	560
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	561 annotation of breakpoints with genes
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	562 increased sensitivity for breakpoints at splice-sites
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	563 calculation of transcriptomic distances
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	564 determining the putative orientation of fused genes (i.e., 5' and 3' end)
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	565 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	566
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	567 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).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	568
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	569
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	570 - Blacklist
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	571
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	572 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	573
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	574 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	575
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	576 Blacklists for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/blacklist_*.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	577
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	578 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:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	579 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	580 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	581 * the name of a gene given in the provided annotation.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	582
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	583 In addition, special keywords are allowed for the second column:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	584 * any: Discard all events if one of the breakpoints matches the given region.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	585 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	586 * split_read_acceptor: Discard events only supported by split reads, if all of them have their clipped segment in the given region.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	587 * split_read_any: Discard events only supported by split reads, regardless of where the anchor is.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	588 * discordant_mates: Discard fusions, if they are only supported by discordant mates (no split reads).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	589 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	590 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	591 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	592 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	593
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	594
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	595 - Known fusions
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	596
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	597 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	598
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	599 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_*.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	600
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	601 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:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	602
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	603 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	604 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	605 * the name of a gene given in the provided annotation.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	606
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	607 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	608
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	609
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	610 - Tags
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	611
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	612 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	613
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	614 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	615
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	616 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:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	617
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	618 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	619 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	620 * the name of a gene given in the provided annotation.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	621
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	622 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	623
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	624 - Protein domains
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	625
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	626 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	627
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	628 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_*.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	629
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	630 The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	631 * Name=PROTEIN_DOMAIN_NAME;
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	632 * gene_id=GENE_ID;
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	633 * gene_name=GENE_NAME
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	634
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	635 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	636
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	637 - Structural variant calls from WGS
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	638
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	639 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:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	640
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	641 Certain filters are overruled or run with extra sensitive settings, when an event is confirmed by WGS data.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	642 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	643 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	644
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	645 Two file formats are accepted: a simple four-column format and the standard Variant Call Format (VCF). The format is detected automatically.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	646
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	647 * 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:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	648
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	649 + downstream or +: the fusion partner is fused downstream of the breakpoint, i.e., at a coordinate higher than the breakpoint
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	650 + upstream or -: the fusion partner is fused at a coordinate lower than the breakpoint
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	651
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	652 Example:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	653
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	654 ::
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	655
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	656 =========== =========== =========== ===========
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	657 5-prime 3-prime orientation orientation
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	658 =========== =========== =========== ===========
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	659 1:54420491 6:9248349 + -
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	660 20:46703288 20:46734546 - +
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	661 17:61499820 20:45133874 + +
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	662 3:190967119 7:77868317 - -
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	663 =========== =========== =========== ===========
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	664
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	665
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	666 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	667
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	668 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	669
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	670 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	671
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	672
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	673 OPTIONS
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	674
5 5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	675 - Arriba: https://github.com/suhrig/arriba/wiki/07-Command-line-options#arriba
5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	676 - Visualization: https://github.com/suhrig/arriba/wiki/07-Command-line-options#draw_fusionsr
5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	677 - RNA STAR: https://github.com/suhrig/arriba/wiki/03-Workflow
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	678
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	679
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	680 OUTPUTS
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	681
5 5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	682 See: https://github.com/suhrig/arriba/wiki/05-Output-files
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	683
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	684 - fusions.tsv
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	685
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	686 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:
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	687
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	688 * 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 (.).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	689
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	690 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	691
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	692 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	693
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	694 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	695
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	696 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	697
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	698 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	699
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	700 * discordant_mates : This column contains the number of pairs (fragments) of discordant mates (a.k.a. spanning reads or bridge reads) supporting the fusion.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	701
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	702 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	703
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	704 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	705
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	706 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	707
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	708 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	709
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	710 * 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 (\|).
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	711
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	712 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	713
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	714 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	715
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	716 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	717
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	718 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	719
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	720 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	721
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	722 * 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	723
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	724 * 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 ?.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	725
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	726 * read_identifiers : This column contains the names of the supporting reads separated by commas.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	727
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	728 - fusions.discarded.tsv
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	729
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	730 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.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	731
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	732
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	733 VISUALIZATION
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	734
5 5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	735 See: https://github.com/suhrig/arriba/wiki/06-Visualization
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	736
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	737 - fusions.pdf
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	738
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	739 A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint.
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	740
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	741 .. image:: draw-fusions-example.png
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	742 :width: 800
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	743 :height: 467
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	744
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	745
5 5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	746 .. _Arriba: https://github.com/suhrig/arriba/wiki/01-Home
5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	747 .. _INPUTS: https://github.com/suhrig/arriba/wiki/04-Input-files
5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	748 .. _OUTPUTS: https://github.com/suhrig/arriba/wiki/05-Output-files
5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	749 .. _VISUALIZATION: https://github.com/suhrig/arriba/wiki/06-Visualization
5e03d09d5fdc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 2d69e621036bf155e02189d4a9a8aa9ee24536e0 iuc parents: 4 diff changeset	750 .. _OPTIONS: https://github.com/suhrig/arriba/wiki/07-Command-line-options
0 fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	751
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	752 ]]></help>
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	753 <expand macro="citations" />
fe0e1083cfd0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	754 </tool>

Mercurial > repos > iuc > arriba

annotate arriba.xml @ 5:5e03d09d5fdc draft default tip