arriba: arriba.xml annotate

annotate arriba.xml @ 5:01ccd366690d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 3a528b3f87cff585baf4abb8ebe0be95a24044ea

author	iuc
date	Wed, 25 Oct 2023 08:24:37 +0000
parents	f6b8b38636a4
children

rev	line source
0 a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	3 <macros>
a24ca22b906e 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>
a24ca22b906e 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">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	6 <actions>
a24ca22b906e 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" />
a24ca22b906e 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" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	9 </actions>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	10 </xml>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	13 </macros>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	14 <expand macro="requirements" />
a24ca22b906e 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" />
a24ca22b906e 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[
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	17 @GENOME_SOURCE@
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	18 @GTF_SOURCE@
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	19 #set $filter_list = []
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	20 #if $options.filters
a24ca22b906e 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(',')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	22 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	23 #if $blacklist
a24ca22b906e 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')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	25 #set $blacklist_file = 'blacklist.tsv.gz'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	26 ln -sf '$blacklist' $blacklist_file &&
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	27 #else
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	29 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	30 #else
a24ca22b906e 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
a24ca22b906e 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')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	33 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	34 #end if
a24ca22b906e 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)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	36 #if $known_fusions
a24ca22b906e 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')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	38 #set $known_fusions_file = 'known_fusions.tsv.gz'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	39 ln -sf '$known_fusions' $known_fusions_file &&
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	40 #else
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	42 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	43 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	44 #if $tags
a24ca22b906e 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')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	46 #set $tags_file = 'tags.tsv.gz'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	47 ln -sf '$tags' $tags_file &&
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	48 #else
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	49 #set $tags_file = $tags
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	50 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	51 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	52 arriba
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	53 -x '$input'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	54 #if $chimeric
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	55 -c '$chimeric'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	56 #end if
a24ca22b906e 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 4f1efcc055d5 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 a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	59 #if $blacklist
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	60 -b '$blacklist_file'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	61 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	62 #if $filters
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	63 -f '$filters'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	64 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	65 #if $protein_domains
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	66 -p '$protein_domains'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	67 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	68 #if $known_fusions
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	69 -k '$known_fusions_file'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	70 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	71 #if $tags
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	72 -t '$tags_file'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	73 #end if
1 4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	74 #if str($wgs_cond.use_wgs) == "yes"
4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	75 -d '$wgs_cond.wgs'
2 add230dddd52 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 4f1efcc055d5 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 a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	78 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	79 #end if
a24ca22b906e 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 4f1efcc055d5 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 a24ca22b906e 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 4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f iuc parents: 0 diff changeset	83 #end if
4f1efcc055d5 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 a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	85 #if $options.gtf_features
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	86 -G '$options.gtf_features'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	87 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	88 #if $options.strandedness
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	89 -s $options.strandedness
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	90 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	91 #if $options.genome_contigs
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	92 -i '$options.genome_contigs'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	93 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	94 #if $options.viral_contigs
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	95 -v '$options.viral_contigs'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	96 #end if
a24ca22b906e 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)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	98 -E $options.max_evalue
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	99 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	100 #if str($options.min_supporting_reads)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	101 -S $options.min_supporting_reads
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	102 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	103 #if str($options.max_mismappers)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	104 -m $options.max_mismappers
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	105 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	106 #if str($options.max_homolog_identity)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	107 -L $options.max_homolog_identity
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	108 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	109 #if str($options.homopolymer_length)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	110 -H $options.homopolymer_length
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	111 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	112 #if str($options.read_through_distance)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	113 -R $options.read_through_distance
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	114 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	115 #if str($options.min_anchor_length)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	116 -A $options.min_anchor_length
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	117 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	118 #if str($options.many_spliced_events)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	119 -M $options.many_spliced_events
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	120 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	121 #if str($options.max_kmer_content)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	122 -K $options.max_kmer_content
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	123 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	124 #if str($options.max_mismatch_pvalue)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	125 -V $options.max_mismatch_pvalue
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	126 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	127 #if str($options.fragment_length)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	128 -F $options.fragment_length
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	129 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	130 #if str($options.max_reads)
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	132 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	133 #if $options.quantile
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	134 -Q $options.quantile
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	135 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	136 #if str($options.exonic_fraction)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	137 -e $options.exonic_fraction
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	138 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	139 #if str($options.top_n)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	140 -T $options.top_n
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	141 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	142 #if str($options.covered_fraction)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	143 -C $options.covered_fraction
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	144 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	145 #if str($options.max_itd_length)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	146 -l $options.max_itd_length
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	147 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	148 #if str($options.min_itd_allele_fraction)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	149 -z $options.min_itd_allele_fraction
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	150 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	151 #if str($options.min_itd_supporting_reads)
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	153 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	154 $options.duplicate_marking
a24ca22b906e 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
a24ca22b906e 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 f6b8b38636a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078 iuc parents: 2 diff changeset	157 #if $output_fusion_bams or str($visualization.do_viz) == "yes"
0 a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	160 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	161 #if $output_fusions_vcf
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	162 && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	163 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	164 #if $output_fusion_bams
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	165 && mkdir fusion_bams
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	166 && extract_fusion-supporting_alignments.sh fusions.tsv Aligned.sortedByCoord.out.bam 'fusion_bams/fusion'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	167 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	168 #if str($visualization.do_viz) == "yes"
a24ca22b906e 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'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	170 && @DRAW_FUSIONS@
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	171 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	172 ]]></command>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	173 <inputs>
a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	176 </param>
a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	179 </param>
a24ca22b906e 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" />
a24ca22b906e 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" />
a24ca22b906e 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."/>
a24ca22b906e 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"/>
a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	186 </param>
a24ca22b906e 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."
a24ca22b906e 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 4f1efcc055d5 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 a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	193 </param>
a24ca22b906e 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 4f1efcc055d5 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 a24ca22b906e 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."/>
a24ca22b906e 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"
a24ca22b906e 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."/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	199 </when>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	200 <when value="no"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	201 </conditional>
a24ca22b906e 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">
a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	206 </param>
a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	213 </param>
a24ca22b906e 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">
a24ca22b906e 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.
a24ca22b906e 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".
a24ca22b906e 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.
a24ca22b906e 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_*
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	219 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	220 <validator type="regex" message="not a valid contig name">^((@GENOME_CONTIG@\|@VIRAL_CONTIG@)([,\s]\s(@GENOME_CONTIG@\|@VIRAL_CONTIG@)))</validator>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	221 </param>
a24ca22b906e 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">
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	225 Default: AC_* NC_*
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	226 </help>
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	228 </param>
a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	267 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	268
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	276 Default: 0.300000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	277 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	278 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	279
a24ca22b906e 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">
a24ca22b906e 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).
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	282 Default: 2
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	283 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	284 </param>
a24ca22b906e 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">
a24ca22b906e 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,
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	288 Default: 0.800000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	289 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	290 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	294 Default: 0.300000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	295 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	296 </param>
a24ca22b906e 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">
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	299 Default: 6
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	300 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	301 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	305 Default: 10000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	306 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	307 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	314 Default: 23
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	315 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	316 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	320 Default: 4
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	321 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	322 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	327 Default: 0.600000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	328 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	329 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	330
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	335 Default: 0.010000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	336 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	337 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	338
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	344 Default: 200
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	345 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	346 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	351 inaccurate, obviously.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	352 Default: 300
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	353 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	354 </param>
a24ca22b906e 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">
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	358 Default: 0.998000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	359 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	360 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	367 Default: 0.330000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	368 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	369 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	370
a24ca22b906e 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">
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	373 Default: 5
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	374 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	375 </param>
a24ca22b906e 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">
a24ca22b906e 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,
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	379 Default: 0.050000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	380 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	381 </param>
a24ca22b906e 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">
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	384 Default: 100
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	385 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	386 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	389 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	390 </param>
a24ca22b906e 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">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	392 <help> Default: 10
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	393 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	394 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	399 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	400 </param>
a24ca22b906e 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">
a24ca22b906e 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',
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	406 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	407 </param>
a24ca22b906e 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">
a24ca22b906e 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
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	411 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	412 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	413 </section>
a24ca22b906e 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"/>
a24ca22b906e 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"/>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	417 <conditional name="visualization">
a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	421 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	422 <when value="yes">
a24ca22b906e 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" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	424 </when>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	425 <when value="no"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	426 </conditional>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	427 </inputs>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	428 <outputs>
a24ca22b906e 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 ${on_string}: fusions.tsv" from_work_dir="fusions.tsv">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	430 <expand macro="fusion_actions" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	431 </data>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	432
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	433 <data name="discarded_fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	434 <filter> output_fusions_discarded == True</filter>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	435 <expand macro="fusion_actions" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	436 </data>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	437 <data name="fusions_vcf" format="vcf" label="${tool.name} on ${on_string}: fusions.vcf" from_work_dir="fusions.vcf">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	438 <filter> output_fusions_vcf == True</filter>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	439 </data>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	440 <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	441 <discover_datasets pattern="(?P<name>fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/>
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	443 </collection>
a24ca22b906e 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">
a24ca22b906e 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>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	446 </data>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	447 </outputs>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	448 <tests>
a24ca22b906e 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 f6b8b38636a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078 iuc parents: 2 diff changeset	450 <test expect_num_outputs="3">
0 a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	452 <conditional name="genome">
a24ca22b906e 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"/>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	455 </conditional>
a24ca22b906e 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">
a24ca22b906e 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"/>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	459 </conditional>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	461 <conditional name="visualization">
a24ca22b906e 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"/>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	464 </conditional>
a24ca22b906e 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">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	466 <assert_contents>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	468 </assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	469 </output>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	470 </test>
a24ca22b906e 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 f6b8b38636a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078 iuc parents: 2 diff changeset	472 <test expect_num_outputs="4">
0 a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	474 <conditional name="genome">
5 01ccd366690d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 3a528b3f87cff585baf4abb8ebe0be95a24044ea iuc parents: 3 diff changeset	475 <param name="genome_source" value="cached"/>
01ccd366690d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 3a528b3f87cff585baf4abb8ebe0be95a24044ea iuc parents: 3 diff changeset	476 <param name="ref_file" value="genome_id"/>
0 a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	477 </conditional>
a24ca22b906e 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">
a24ca22b906e 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"/>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	481 </conditional>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	483 <conditional name="visualization">
a24ca22b906e 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"/>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	486 </conditional>
a24ca22b906e 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">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	488 <assert_contents>
a24ca22b906e 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"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	490 </assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	491 </output>
a24ca22b906e 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">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	493 <assert_contents>
a24ca22b906e 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" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	495 </assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	496 </output>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	497 </test>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	498
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	499 </tests>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	500 <help><![CDATA[
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	501 Arriba
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	502
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	503
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	506
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	507
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	508 INPUTS
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	509
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	510 See: https://arriba.readthedocs.io/en/latest/input-files/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	511
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	512 - Alignments
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	513
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	515
a24ca22b906e 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:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	517
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	518 * --sjdbOverhang 250
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	519
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	520
a24ca22b906e 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 ::
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	522
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	523 * --outSAMunmapped Within
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	524 * --outFilterMultimapNmax 50
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	525 * --peOverlapNbasesMin 10
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	526 * --alignSplicedMateMapLminOverLmate 0.5
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	528 * --chimSegmentMin 10
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	529 * --chimOutType WithinBAM HardClip
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	530 * --chimJunctionOverhangMin 10
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	531 * --chimScoreDropMax 30
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	532 * --chimScoreJunctionNonGTAG 0
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	533 * --chimScoreSeparation 1
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	534 * --chimSegmentReadGapMax 3
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	535 * --chimMultimapNmax 50
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	536
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	537
a24ca22b906e 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):
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	539
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	543
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	545
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	547
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	548
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	549 - Assembly
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	550
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	552
a24ca22b906e 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).
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	554
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	556
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	557 - Annotation
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	558
a24ca22b906e 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:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	560
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e 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)
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	566
a24ca22b906e 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).
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	568
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	569
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	570 - Blacklist
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	571
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	573
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	575
a24ca22b906e 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_*.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	577
a24ca22b906e 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:
a24ca22b906e 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.
a24ca22b906e 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).
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	582
a24ca22b906e 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:
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e 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).
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	593
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	594
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	595 - Known fusions
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	596
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	598
a24ca22b906e 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_*.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	600
a24ca22b906e 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:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	602
a24ca22b906e 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.
a24ca22b906e 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).
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	606
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	608
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	609
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	610 - Tags
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	611
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	613
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	615
a24ca22b906e 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:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	617
a24ca22b906e 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).
a24ca22b906e 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).
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	621
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	623
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	624 - Protein domains
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	625
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	627
a24ca22b906e 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_*.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	629
a24ca22b906e 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:
a24ca22b906e 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;
a24ca22b906e 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;
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	634
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	636
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	638
a24ca22b906e 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:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	640
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	644
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	646
a24ca22b906e 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:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	648
a24ca22b906e 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
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	651
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	652 Example:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	653
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	654 ::
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	655
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	656 =========== =========== =========== ===========
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	658 =========== =========== =========== ===========
a24ca22b906e 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 + -
a24ca22b906e 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 - +
a24ca22b906e 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 + +
a24ca22b906e 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 - -
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	663 =========== =========== =========== ===========
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	664
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	665
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	667
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	669
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	671
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	672
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	673 OPTIONS
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	674
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	675 - Arriba: https://arriba.readthedocs.io/en/latest/command-line-options/#arriba
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	676 - Visualization: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	677 - RNA STAR: https://arriba.readthedocs.io/en/latest/workflow/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	678
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	679
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	680 OUTPUTS
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	681
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	682 See: https://arriba.readthedocs.io/en/latest/output-files/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	683
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	684 - fusions.tsv
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	685
a24ca22b906e 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:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	687
a24ca22b906e 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 (.).
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	689
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	691
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	693
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	695
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	697
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	699
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	701
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	703
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	705
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	707
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	709
a24ca22b906e 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 (\|).
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	711
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	713
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	715
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	717
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	719
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	721
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	723
a24ca22b906e 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 ?.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	725
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	727
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	728 - fusions.discarded.tsv
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	729
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	731
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	732
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	733 VISUALIZATION
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	734
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	735 See: https://arriba.readthedocs.io/en/latest/visualization/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	736
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	737 - fusions.pdf
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	738
a24ca22b906e 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.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	740
a24ca22b906e 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
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	742 :width: 800
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	743 :height: 467
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	744
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	745
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	746 .. _Arriba: https://arriba.readthedocs.io/en/latest/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	747 .. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	748 .. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	749 .. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	750 .. _OPTIONS: https://arriba.readthedocs.io/en/latest/command-line-options/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	751
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	752 ]]></help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823 iuc parents: diff changeset	753 <expand macro="citations" />
a24ca22b906e 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 @ 5:01ccd366690d draft default tip