annotate arriba.xml @ 10:c58d1774c762 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
author jjohnson
date Fri, 11 Feb 2022 19:04:06 +0000
parents 8c4c97fd0555
children 8ed8af5836d1
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1 <tool id="arriba" name="Arriba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
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2 <description>detect gene fusions from STAR aligned RNA-Seq data</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @GENOME_SOURCE@
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10 #if str($input_params.input_source) == "use_fastq"
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11 #set $readFilesCommand = ''
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12 #set $read2 = ''
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13 #if str($input_params.singlePaired.sPaired) == 'paired_collection':
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14 #if $input_params.singlePaired.input.forward.is_of_type('fastq.gz', 'fastqsanger.gz'):
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15 #set $readFilesCommand = '--readFilesCommand zcat'
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16 #set read1 = 'input_1.fastq.gz'
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17 #set read2 = 'input_2.fastq.gz'
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18 #else
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19 #set read1 = 'input_1.fastq'
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20 #set read2 = 'input_2.fastq'
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21 #end if
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22 ln -sf '${$input_params.singlePaired.input.forward}' ${read1} &&
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23 ln -sf '${$input_params.singlePaired.input.reverse}' ${read2} &&
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24 #else
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25 #if $input_params.singlePaired.input1.is_of_type('fastq.gz', 'fastqsanger.gz'):
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26 #set $readFilesCommand = '--readFilesCommand zcat'
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27 #set read1 = 'input_1.fastq.gz'
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28 #else
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29 #set read1 = 'input_1.fastq'
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30 #end if
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31 ln -sf '$input_params.singlePaired.input1' ${read1} &&
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32 #if str($input_params.singlePaired.sPaired) == 'paired':
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33 #set $read2 = $read1.replace('1','2')
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34 ln -sf '$input_params.singlePaired.input2' ${read2} &&
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35 #end if
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36 #end if
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37 #if str($input_params.index.index_source) == "history"
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38 #set $star_index_dir = $input_params.index.star_index.extra_files_path
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39 #else
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40 #set $star_index_dir = $input_params.index.arriba_ref.fields.star_index
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41 #end if
1
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42 STAR
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43 --runThreadN \${GALAXY_SLOTS:-1}
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44 --genomeDir $star_index_dir
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45 --genomeLoad NoSharedMemory
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46 --readFilesIn $read1 $read2
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47 $readFilesCommand
1
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48 --outStd BAM_Unsorted
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49 --outSAMtype BAM Unsorted
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50 --outSAMunmapped Within
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51 --outBAMcompression 0
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52 --outFilterMultimapNmax 50
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53 --peOverlapNbasesMin 10
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54 --alignSplicedMateMapLminOverLmate 0.5
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55 --alignSJstitchMismatchNmax 5 -1 5 5
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56 --chimSegmentMin 10
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57 --chimOutType WithinBAM HardClip
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58 --chimJunctionOverhangMin 10
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59 --chimScoreDropMax 30
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60 --chimScoreJunctionNonGTAG 0
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61 --chimScoreSeparation 1
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62 --chimSegmentReadGapMax 3
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63 --chimMultimapNmax 50
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64 | tee Aligned.out.bam |
0
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65 arriba
1
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66 -x '/dev/stdin'
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67 #else
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68 arriba
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69 -x '$input_params.input'
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70 #if $input_params.chimeric
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71 -c '$input_params.chimeric'
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72 #end if
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73 #end if
0
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74 -a '$genome_assembly'
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75 -g '$genome_annotation'
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76 #if $blacklist
1
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77 -b '$blacklist'
4
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78 #else
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79 -f 'blacklist'
1
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80 #end if
4
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81 #if $protein_domains
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
parents:
diff changeset
82 -p '$protein_domains'
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
83 #end if
4
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
jjohnson
parents: 3
diff changeset
84 #if $known_fusions
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
parents:
diff changeset
85 -k '$known_fusions'
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
86 #end if
4
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
jjohnson
parents: 3
diff changeset
87 #if $tags
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
parents:
diff changeset
88 -t '$tags'
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
89 #end if
6
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
90 #if str($wgs.use_wgs) == "yes"
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
91 -d '$wgs.wgs'
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
92 #if $wgs.max_genomic_breakpoint_distance
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
93 -D $wgs.max_genomic_breakpoint_distance
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
94 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
95 #end if
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
parents:
diff changeset
96 -o fusions.tsv
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
jjohnson
parents: 4
diff changeset
97 #if $output_fusions_discarded
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
parents:
diff changeset
98 -O fusions.discarded.tsv
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
jjohnson
parents: 4
diff changeset
99 #end if
6
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
100 ## Arriba options
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
101 #if $options.gtf_features
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
102 -G $options.gtf_features
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
103 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
104 #if $options.strandedness
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
105 -s $options.strandedness
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
106 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
107 #if $options.genome_contigs
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
108 -i $options.genome_contigs
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
109 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
110 #if $options.viral_contigs
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
111 -v $options.viral_contigs
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
112 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
113 #if $options.max_evalue
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
114 -E $options.max_evalue
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
115 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
116 #if $options.min_supporting_reads
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
117 -S $options.min_supporting_reads
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
118 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
119 #if $options.max_mismappers
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
120 -m $options.max_mismappers
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
121 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
122 #if $options.max_homolog_identity
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
123 -L $options.max_homolog_identity
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
124 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
125 #if $options.homopolymer_length
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
126 -H $options.homopolymer_length
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
127 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
128 #if $options.read_through_distance
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
129 -R $options.read_through_distance
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
130 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
131 #if $options.min_anchor_length
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
132 -A $options.min_anchor_length
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
133 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
134 #if $options.many_spliced_events
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
135 -M $options.many_spliced_events
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
136 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
137 #if $options.max_kmer_content
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
138 -m $options.max_kmer_content
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
139 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
140 #if $options.max_mismatch_pvalue
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
141 -V $options.max_mismatch_pvalue
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
142 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
143 #if $options.fragment_length
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
144 -F $options.fragment_length
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
145 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
146 #if $options.max_reads
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
147 -U $options.max_reads
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
148 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
149 #if $options.quantile
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
150 -Q $options.quantile
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
151 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
152 #if $options.exonic_fraction
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
153 -e $options.exonic_fraction
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
154 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
155 #if $options.top_n
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
156 -T $options.top_n
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
157 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
158 #if $options.covered_fraction
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
159 -C $options.covered_fraction
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
160 #end if
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
161 #if $options.max_itd_length
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
162 -l $options.max_itd_length
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
163 #end if
10
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents: 9
diff changeset
164 #if $options.min_itd_allele_fraction
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents: 9
diff changeset
165 -z $options.min_itd_allele_fraction
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents: 9
diff changeset
166 #end if
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents: 9
diff changeset
167 #if $options.min_itd_supporting_reads
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents: 9
diff changeset
168 -Z $options.min_itd_supporting_reads
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents: 9
diff changeset
169 #end if
6
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
170 $options.duplicate_marking
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
171 $options.fill_discarded_columns
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172 $options.fill_the_gaps
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173 #if str($input_params.input_source) == "use_fastq"
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174 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam
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175 && samtools index Aligned.sortedByCoord.out.bam
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176 #elif str($visualization.do_viz) == "yes"
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177 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam
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178 && samtools index Aligned.sortedByCoord.out.bam
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179 #end if
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180 #if str($visualization.do_viz) == "yes"
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181 #set $fusions = 'fusions.tsv'
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182 && @DRAW_FUSIONS@
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183 #end if
0
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184 ]]></command>
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185 <inputs>
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186 <conditional name="input_params">
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187 <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR">
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188 <option value="use_star">Use output from earlier STAR</option>
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189 <option value="use_fastq">Let Arriba control running STAR</option>
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190 </param>
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191 <when value="use_star">
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192 <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam"/>
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193 <param name="chimeric" argument="-c" type="data" format="sam,bam,cram" optional="true" label="STAR Chimeric.out.sam">
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194 <help><![CDATA[ only required, if STAR was run with the parameter '--chimOutType SeparateSAMold' ]]></help>
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195 </param>
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196 </when>
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197 <when value="use_fastq">
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198 <conditional name="singlePaired">
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199 <param name="sPaired" type="select" label="Single-end or paired-end reads">
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200 <option value="single" selected="true">Single-end</option>
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201 <option value="paired">Paired-end (as individual datasets)</option>
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202 <option value="paired_collection">Paired-end (as collection)</option>
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203 </param>
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204 <when value="single">
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205 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file"/>
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206 </when>
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207 <when value="paired">
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208 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, forward reads"/>
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209 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, reverse reads"/>
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210 </when>
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211 <when value="paired_collection">
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212 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ/FASTA paired reads"/>
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213 </when>
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214 </conditional>
2
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215 <conditional name="index">
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216 <param name="index_source" type="select" label="Arriba STAR index source">
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217 <option value="history">Arriba STAR index from your history</option>
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218 <option value="cached">Use a built-in Arriba STAR index</option>
2
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219 </param>
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220 <when value="history">
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221 <param name="star_index" argument="--genomeDir" type="data" format="txt" label="Arriba STAR index"
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222 help="generated by: Arriba Reference"/>
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223 </when>
9
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224 <when value="cached">
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225 <param name="arriba_ref" type="select" label="Arriba STAR index">
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226 <options from_data_table="arriba_indexes">
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227 </options>
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228 </param>
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229 </when>
2
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230 </conditional>
9
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231
1
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232 </when>
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233 </conditional>
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234 <expand macro="genome_source" />
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235 <param name="blacklist" argument="-b" type="data" format="tabular,tabular.gz" optional="true" label="File containing blacklisted ranges."/>
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236 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
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237 <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz" optional="true" label="File containing known fusions">
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238 <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
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239 </param>
4
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240 <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."
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241 help="This can be the known fusions if that input has a third column with a name"/>
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242 <conditional name="wgs">
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243 <param name="use_wgs" type="select" label="Use whole-genome sequencing data">
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244 <option value="no">no</option>
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245 <option value="yes">Yes</option>
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246 </param>
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247 <when value="yes">
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248 <param name="wgs" argument="-d" type="data" format="tabular" label="whole-genome sequencing structural variant data"
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249 help="These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence."/>
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250 <param name="max_genomic_breakpoint_distance" argument="-D" type="integer" value="100000" label="Max genomic breakpoint distance"
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251 help="determines how far a genomic breakpoint may be away from a transcriptomic breakpoint to consider it as a related event."/>
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252 </when>
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253 <when value="no"/>
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254 </conditional>
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255 <section name="options" expanded="false" title="Arriba Options">
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256 <param name="gtf_features" argument="-G" type="text" value="" optional="true" label="Names of features in the GTF annotation file">
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257 <help>Commma or SPACE separated list, default: gene_name=gene_name gene_id=gene_id transcript_id=transcript_id feature_exon=exon feature_CDS=CDS</help>
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258 <validator type="regex" message="">^(gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=[^ ,]+([ ,](gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=[^ ,]+)?$</validator>
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259 </param>
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260 <param name="strandedness" argument="-s" type="select" optional="true" label="Whether a strand-specific protocol was used for library preparation">
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261 <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>
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262 <option value="auto">auto</option>
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263 <option value="yes">yes</option>
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264 <option value="no">no</option>
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265 <option value="reverse">reverse</option>
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266 </param>
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267 <param name="genome_contigs" argument="-i" type="text" value="" optional="true" label="Comma-/space-separated list of interesting contigs">
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268 <help>Comma-/space-separated list of interesting contigs.
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269 Fusions between genes on other contigs are ignored. Contigs can be specified with or without the prefix "chr".
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270 Asterisks (*) are treated as wild-cards.
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271 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_*
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272 </help>
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273 </param>
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274 <param name="viral_contigs" argument="-v" type="text" value="" optional="true" label="Comma-/space-separated list of viral contigs">
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275 <help>Comma-/space-separated list of viral contigs.
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276 Asterisks (*) are treated as wild-cards.
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277 Default: AC_* NC_*
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278 </help>
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279 </param>
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280 <param name="max_evalue" argument="-E" type="float" value="" optional="true" label="Max e-value threahold">
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281 <help>Arriba estimates the number of fusions with a given number of supporting
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282 reads which one would expect to see by random chance. If the expected number
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283 of fusions (e-value) is higher than this threshold, the fusion is
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284 discarded by the 'relative_support' filter. Note: Increasing this
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285 threshold can dramatically increase the number of false positives and may
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286 increase the runtime of resource-intensive steps. Fractional values are possible.
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287 Default: 0.300000
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288 </help>
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289 </param>
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290
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291 <param name="min_supporting_reads" argument="-S" type="integer" value="" min="1" optional="true" label="Min supporting reads">
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292 <help>discard all fusions with fewer than this many supporting reads (split reads and discordant mates combined).
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293 Default: 2
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294 </help>
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295 </param>
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296 <param name="max_mismappers" argument="-m" type="float" value="" min="0." max="1.0" optional="true" label="Max mismappers threshold">
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297 <help>When more than this fraction of supporting reads turns out to be mismappers,
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298 the 'mismappers' filter discards the fusion.
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299 Default: 0.800000
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300 </help>
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301 </param>
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302 <param name="max_homolog_identity" argument="-L" type="float" value="" min="0." max="1.0" optional="true" label="Max homologs identity threshold">
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303 <help>Genes with more than the given fraction of sequence identity are
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304 considered homologs and removed by the 'homologs' filter.
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305 Default: 0.300000
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306 </help>
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307 </param>
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308 <param name="homopolymer_length" argument="-H" type="integer" value="" min="1" optional="true" label="Homopolymer length">
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309 <help>The 'homopolymer' filter removes breakpoints adjacent to homopolymers of the given length or more.
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310 Default: 6
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311 </help>
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312 </param>
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313 <param name="read_through_distance" argument="-R" type="integer" value="" min="1" optional="true" label="Read-through distance">
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314 <help>The 'read_through' filter removes read-through fusions
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315 where the breakpoints are less than the given distance away from each other.
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316 Default: 10000
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317 </help>
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318 </param>
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319 <param name="min_anchor_length" argument="-A" type="integer" value="" min="1" optional="true" label="Min anchor length">
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320 <help>Alignment artifacts are often characterized by split reads coming
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321 from only one gene and no discordant mates. Moreover, the split
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322 reads only align to a short stretch in one of the genes. The
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323 'short_anchor' filter removes these fusions. This parameter sets
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324 the threshold in bp for what the filter considers short.
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325 Default: 23
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326 </help>
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327 </param>
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328 <param name="many_spliced_events" argument="-M" type="integer" value="" min="1" optional="true" label="Many spliced events">
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329 <help>The 'many_spliced' filter recovers fusions between genes that
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330 have at least this many spliced breakpoints.
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331 Default: 4
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332 </help>
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333 </param>
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334 <param name="max_kmer_content" argument="-m" type="float" value="" min="0." max="1.0" optional="true" label="Max kmer content">
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335 <help>The 'low_entropy' filter removes reads with repetitive 3-mers. If
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336 the 3-mers make up more than the given fraction of the sequence, then
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337 the read is discarded.
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338 Default: 0.600000
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339 </help>
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340 </param>
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341
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342 <param name="max_mismatch_pvalue" argument="-V" type="float" value="" optional="true" label="Max mismatchrpvalue threahold">
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343 <help>The 'mismatches' filter uses a binomial model to calculate a
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344 p-value for observing a given number of mismatches in a read.
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345 If the number of mismatches is too high, the read is discarded.
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346 Default: 0.010000
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347 </help>
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348 </param>
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349
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350 <param name="fragment_length" argument="-F" type="integer" value="" min="1" optional="true" label="Single-end fragment length">
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351 <help>When paired-end data is given, the fragment length is estimated
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352 automatically and this parameter has no effect. But when single-end
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353 data is given, the mean fragment length should be specified to
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354 effectively filter fusions that arise from hairpin structures.
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355 Default: 200
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356 </help>
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357 </param>
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358 <param name="max_reads" argument="-U" type="integer" value="" min="1" optional="true" label="Max reads">
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359 <help>Subsample fusions with more than the given number of supporting reads. This
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360 improves performance without compromising sensitivity, as long as the
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361 threshold is high. Counting of supporting reads beyond the threshold is
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362 inaccurate, obviously.
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363 Default: 300
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364 </help>
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365 </param>
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366 <param name="quantile" argument="-Q" type="float" value="" min="0." max="1.0" optional="true" label="Quantile">
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367 <help>Highly expressed genes are prone to produce artifacts during library preparation.
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368 Genes with an expression above the given quantile are eligible for filtering by the 'in_vitro' filter.
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369 Default: 0.998000
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370 </help>
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371 </param>
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372 <param name="exonic_fraction" argument="-e" type="float" value="" min="0." max="1.0" optional="true" label="Exonic fraction">
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373 <help>The breakpoints of false-positive predictions of intragenic events
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374 are often both in exons. True predictions are more likely to have at
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375 least one breakpoint in an intron, because introns are larger.
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376 If the fraction of exonic sequence between two breakpoints is smaller than
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377 the given fraction, the 'intragenic_exonic' filter discards the event.
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378 Default: 0.330000
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379 </help>
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380 </param>
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381
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382 <param name="top_n" argument="-T" type="integer" value="" min="1" optional="true" label="top N viral contigs">
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383 <help>Only report viral integration sites of the top N most highly expressed viral contigs.
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384 Default: 5
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385 </help>
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386 </param>
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387 <param name="covered_fraction" argument="-C" type="float" value="" min="0." max="1.0" optional="true" label="Covered fraction">
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388 <help>Ignore virally associated events if the virus is not fully expressed,
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389 i.e., less than the given fraction of the viral contig is transcribed.
10
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390 Default: 0.050000
6
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391 </help>
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392 </param>
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393 <param name="max_itd_length" argument="-l" type="integer" value="" min="1" optional="true" label="Maximum length of internal tandem duplications">
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394 <help>Note: Increasing this value beyond the default can impair performance and lead to many false positives.
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395 Default: 100
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396 </help>
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397 </param>
10
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398 <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">
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399 <help> Default: 0.070000
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400 </help>
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401 </param>
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402 <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">
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403 <help> Default: 10
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404 </help>
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405 </param>
6
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406 <param name="duplicate_marking" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Use aligners duplicate marking">
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407 <help>Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a
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408 preceding program using the BAM_FDUP flag. This makes sense when unique molecular
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409 identifiers (UMI) are used.
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410 </help>
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411 </param>
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412 <param name="fill_discarded_columns" argument="-X" type="boolean" truevalue="-X" falsevalue="" checked="false" label="Fill all fusion.discarded.tsv columns">
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413 <help>To reduce the runtime and file size, by default, the columns 'fusion_transcript',
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414 'peptide_sequence', and 'read_identifiers' are left empty in the file containing
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415 discarded fusion candidates (see parameter -O). When this flag is set, this extra
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416 information is reported in the discarded fusions file.
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417 </help>
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418 </param>
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419 <param name="fill_the_gaps" argument="-I" type="boolean" truevalue="-I" falsevalue="" checked="false" label="Fill fusion transcript gaps from the assembly">
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
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diff changeset
420 <help>If assembly of the fusion transcript sequence from the supporting reads is incomplete
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421 (denoted as '...'), fill the gaps using the assembly sequence wherever possible.
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
jjohnson
parents: 5
diff changeset
422 </help>
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423 </param>
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diff changeset
424 </section>
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
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425 <param name="output_fusions_discarded" argument="-O" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.discarded.tsv"/>
3
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jjohnson
parents: 2
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426 <conditional name="visualization">
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
jjohnson
parents: 2
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427 <param name="do_viz" type="select" label="Generate visualization">
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
jjohnson
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428 <option value="yes">Yes</option>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
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429 <option value="no">no</option>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
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diff changeset
430 </param>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
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431 <when value="yes">
7
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432 <expand macro="visualization_options" />
3
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433 </when>
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434 <when value="no"/>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
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435 </conditional>
6
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diff changeset
436
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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diff changeset
437 </inputs>
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jjohnson
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diff changeset
438 <outputs>
7
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439 <data name="fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>
25d207f7ff83 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
jjohnson
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440 <data name="discarded_fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv">
9
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441 <filter> output_fusions_discarded == True</filter>
5
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jjohnson
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diff changeset
442 </data>
3
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
jjohnson
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443 <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
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444 <filter>input_params['input_source'] == "use_fastq"</filter>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
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445 </data>
4
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parents: 3
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446 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
3
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
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447 <filter>visualization['do_viz'] == "yes"</filter>
2d32e6c86c48 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
jjohnson
parents: 2
diff changeset
448 </data>
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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449 </outputs>
4
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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450 <tests>
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451 <!-- Test 1 - From exisitng BAM -->
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452 <test>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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453 <conditional name="input_params">
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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454 <param name="input_source" value="use_star"/>
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455 <param name="input" ftype="sam" value="Aligned.out.sam"/>
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456 </conditional>
9
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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457 <conditional name="genome">
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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458 <param name="genome_source" value="history"/>
10
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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459 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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460 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
9
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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461 </conditional>
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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462 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
4
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
jjohnson
parents: 3
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463 <conditional name="visualization">
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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464 <param name="do_viz" value="no"/>
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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parents: 4
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465 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
4
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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466 </conditional>
7
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467 <output name="fusions_tsv">
4
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parents: 3
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468 <assert_contents>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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469 <has_text_matching expression="BCR\tABL1"/>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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470 </assert_contents>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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diff changeset
471 </output>
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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472 </test>
5
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473 <!-- Test 2 - From exisitng BAM with protein_domains and visualization -->
9
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474
5
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parents: 4
diff changeset
475 <test>
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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476 <conditional name="input_params">
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
jjohnson
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diff changeset
477 <param name="input_source" value="use_star"/>
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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diff changeset
478 <param name="input" ftype="sam" value="Aligned.out.sam"/>
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diff changeset
479 </conditional>
9
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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diff changeset
480 <conditional name="genome">
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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diff changeset
481 <param name="genome_source" value="history"/>
10
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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482 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
c58d1774c762 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
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483 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
9
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diff changeset
484 </conditional>
7
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diff changeset
485 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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diff changeset
486 <conditional name="visualization">
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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diff changeset
487 <param name="do_viz" value="yes"/>
7
25d207f7ff83 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
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diff changeset
488 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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parents: 4
diff changeset
489 </conditional>
7
25d207f7ff83 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
jjohnson
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diff changeset
490 <output name="fusions_tsv">
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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parents: 4
diff changeset
491 <assert_contents>
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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diff changeset
492 <has_text_matching expression="BCR\tABL1"/>
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
jjohnson
parents: 4
diff changeset
493 </assert_contents>
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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parents: 4
diff changeset
494 </output>
7
25d207f7ff83 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
jjohnson
parents: 6
diff changeset
495 <output name="fusions_pdf">
25d207f7ff83 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
jjohnson
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diff changeset
496 <assert_contents>
25d207f7ff83 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
jjohnson
parents: 6
diff changeset
497 <has_size value= "64000" delta="5000" />
25d207f7ff83 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
jjohnson
parents: 6
diff changeset
498 </assert_contents>
25d207f7ff83 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit e113a79cc67e0bdb168babfe964f34873b2e1303"
jjohnson
parents: 6
diff changeset
499 </output>
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
jjohnson
parents: 4
diff changeset
500 </test>
9
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
parents: 8
diff changeset
501 <!-- Test 3 - From exisitng BAM using cached genome source -->
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
jjohnson
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502 <test>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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503 <conditional name="input_params">
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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504 <param name="input_source" value="use_star"/>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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505 <param name="input" ftype="sam" value="Aligned.out.sam"/>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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506 </conditional>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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507 <conditional name="genome">
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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508 <param name="genome_source" value="cached"/>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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509 <param name="arriba_ref" value="GRCh38+ENSEMBL93"/>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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510 </conditional>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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511 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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512 <conditional name="visualization">
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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513 <param name="do_viz" value="no"/>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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514 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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515 </conditional>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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516 <output name="fusions_tsv">
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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517 <assert_contents>
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518 <has_text_matching expression="BCR\tABL1"/>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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519 </assert_contents>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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parents: 8
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520 </output>
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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521 </test>
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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parents: 4
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522
4
77021ad5037d "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
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parents: 3
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523 </tests>
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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524 <help><![CDATA[
6
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diff changeset
525 **Arriba**
0
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526
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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527
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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parents: 0
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528 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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529 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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530
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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parents: 0
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531
6
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parents: 5
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532 **INPUTS**
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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533
6
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
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534 See: https://arriba.readthedocs.io/en/latest/input-files/
1
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535
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
536 - Alignments
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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537
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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538 Arriba takes the main output file of STAR (Aligned.out.bam) as input (parameter -x). If STAR was run with the parameter --chimOutType WithinBAM, then this file contains all the information needed by Arriba to find fusions. When STAR was run with the parameter --chimOutType SeparateSAMold, the main output file lacks chimeric alignments. Instead, STAR writes them to a separate output file named Chimeric.out.sam. In this case, the file needs to be passed to Arriba via the parameter -c in addition to the main output file Aligned.out.bam.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
539
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
540 Arriba extracts three types of reads from the alignment file(s):
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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541
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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542 * Split-reads, i.e., reads composed of segments which map in a non-linear way. STAR stores such reads as supplementary alignments.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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543 * Discordant mates, i.e., paired-end reads which originate from the same fragment but which align in a non-linear way.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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544 * 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.
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diff changeset
545
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
546 The alignment files can be in SAM, BAM, and CRAM format. They need not be sorted for Arriba to accept them, but doing so comes with benefits: Often, this reduces the file size. And more importantly, the supporting reads of a fusion can be inspected visually using a genome browser like IGV, which typically requires BAM files to be sorted by coordinate.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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547
1
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diff changeset
548 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.
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diff changeset
549
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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550
1
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diff changeset
551 - Assembly
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diff changeset
552
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
553 Arriba takes the assembly as input (parameter -a) to find mismatches between the chimeric reads and the reference genome, as well as to find alignment artifacts and homologous genes.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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554
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
555 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).
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parents: 0
diff changeset
556
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
557 The assembly must be provided in FastA format and may be gzip-compressed. An index with the file extension .fai must exist only if CRAM files are processed.
0
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558
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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559 - Annotation
0
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diff changeset
560
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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561 The gene annotation (parameter -g) is used for multiple purposes:
0
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562
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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563 annotation of breakpoints with genes
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564 increased sensitivity for breakpoints at splice-sites
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565 calculation of transcriptomic distances
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566 determining the putative orientation of fused genes (i.e., 5' and 3' end)
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567 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.
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568
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
569 The script download_references.sh can be used to download the annotation. The available annotation files are listed when the script is run without parameters. The user is not restricted to these annotation files, however. Any annotation can be used as long as its coordinates are compatible with one of the supported assemblies (hg19/hs37d5/GRCh37 or hg38/GRCh38 or mm10/GRCm38).
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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diff changeset
570
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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diff changeset
571
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
572 - Blacklist
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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573
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
574 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.
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jjohnson
parents: 0
diff changeset
575
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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diff changeset
576 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.
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diff changeset
577
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
578 Blacklists for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/blacklist_*.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
parents:
diff changeset
579
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
580 The blacklist is a tab-separated file with two columns and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions between which events are ignored. A region can be:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
581 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). If CONTIG ends on an asterisk (*), the contig with the closest matching name is chosen.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
582 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
583 * the name of a gene given in the provided annotation.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
parents:
diff changeset
584
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
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585 In addition, special keywords are allowed for the second column:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
586 * any: Discard all events if one of the breakpoints matches the given region.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
587 * split_read_donor: Discard fusions only supported by split reads, if all of them have their anchor in the gene given in the first column. This filter is useful for highly mutable loci, which frequently trigger clipped alignments, such as the immunoglobulin loci or the T-cell receptor loci.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
588 * split_read_acceptor: Discard events only supported by split reads, if all of them have their clipped segment in the given region.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
589 * split_read_any: Discard events only supported by split reads, regardless of where the anchor is.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
590 * discordant_mates: Discard fusions, if they are only supported by discordant mates (no split reads).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
591 * low_support: Discard events, which have few supporting reads relative to expression (as determined by the filter relative_support), even if there is other evidence that the fusion might be a true positive, nonetheless. This keyword effectively prevents recovery of speculative events by filters such as spliced or many_spliced.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
592 * filter_spliced: This keyword prevents the filter spliced from being applied to a given region. It is triggered under the same circumstances as the keyword low_support, but additionally requires that the breakpoints be at splice-sites for the event to be discarded. Some breakpoints produce recurrent artifacts, but the second breakpoint is always a different one, such that the pair of breakpoints is not recurrent and cannot be blacklisted. Often, such breakpoints are at splice-sites and the filter spliced tends to recover them. This keyword prevents the filter from doing so.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
593 * not_both_spliced: This keyword discards events, unless both breakpoints are at splice-sites. This is a strict blacklist criterion, which makes sense to apply to genes which are prone to produce artifacts, because they are highly expressed, for example hemoglobins, collagens, or ribosomal genes.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
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594 * read_through: This keyword discards events, if they could arise from read-through transcription, i.e., the supporting reads are oriented like a deletion and are at most 400 kb apart.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
595
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
596
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
597 - Known fusions
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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diff changeset
598
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
599 Arriba can be instructed to be particularly sensitive towards events between certain gene pairs by supplying a list of gene pairs (parameter -k). A number of filters are not applied to these gene pairs. This is useful to improve the detection rate of expected or highly relevant events, such as recurrent fusions. Occassionally, this leads to false positive calls. But if high sensitivity is more important than specificity, this might be acceptable. Events which would be discarded by a filter and were recovered due to being listed in the known fusions list are usually assigned a low confidence.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
600
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
601 Known fusions files for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/known_fusions_*.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
602
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
603 The file has two columns separated by a tab and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions to which very sensitive filtering thresholds are applied. A region can be:
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
parents:
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604
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
605 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). If CONTIG ends on an asterisk (*), the contig with the closest matching name is chosen.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
606 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
607 * the name of a gene given in the provided annotation.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
608
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
609 The order of the given regions is important. The region given in the first column is assumed to denote the 5' end of the fusion and the region in the second column to be the 3' end. If Arriba cannot determine with confidence which gene constitutes the 5' and which the 3' end of a fusion prediction, then the order is ignored and the prediction is rescued in both cases.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
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610
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
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611
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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612 - Tags
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
613
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
614 Arriba can be supplied with a list of user-defined tags using the parameter -t. Whenever a fusion prediction matches the selection criteria for a tag, the column tags is populated with the respective tag. This feature is useful to annotate known oncogenic fusions, for example.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
615
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
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616 The known fusions file shipped with the download package of Arriba can be used for both known fusions and tags. It is constructed in a way that it can be passed as arguments to the parameters -k and -t alike. The former only uses the first two columns, the latter uses all three columns. If a user wants to separate filtering of known fusions and tagging of interesting fusions, different files may be used, however.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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617
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
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618 The file has three columns separated by a tab and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions to be annotated. The first two columns specify the regions to be annotated; the third column the tag that is used for annotation. Some special characters in the tag are replaced with underscores (_) in Arriba's output file. A region can be:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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diff changeset
619
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
diff changeset
620 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
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621 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
parents: 0
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622 * the name of a gene given in the provided annotation.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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623
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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624 The order of the given regions is important. The region given in the first column is assumed to denote the 5' end of the fusion and the region in the second column to be the 3' end.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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diff changeset
625
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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626 - Protein domains
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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627
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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628 Protein domain annotation can be passed to Arriba via the parameter -p. The column retained_protein_domains of Arriba's output file is then populated accordingly.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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629
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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630 Protein domain annotation files for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/protein_domains_*.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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631
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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632 The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes:
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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633 * Name=PROTEIN_DOMAIN_NAME;
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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634 * gene_id=GENE_ID;
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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635 * gene_name=GENE_NAME
2
7420753b0671 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 7dbe725aaa7b4b84d7b14ea52f38f63d362bf09c"
jjohnson
parents: 1
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636
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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637 The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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638
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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639 - Structural variant calls from WGS
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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640
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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641 If whole-genome sequencing (WGS) data is available, the sensitivity and specificity of Arriba can be improved by passing a list of structural variants detected from WGS to Arriba via the parameter -d. This has the following effects:
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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642
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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diff changeset
643 Certain filters are overruled or run with extra sensitive settings, when an event is confirmed by WGS data.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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644 To reduce the false positive rate, Arriba does not report low-confidence events unless they can be matched with a structural variant found in the WGS data.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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645 Both of these behaviors can be disabled by disabling the filters genomic_support and no_genomic_support, respectively. Providing Arriba with a list of structural variant calls then does not influence the calls, but it still has the benefit of filling the columns closest_genomic_breakpoint1 and closest_genomic_breakpoint2 with the breakpoints of the structural variant which is closest to a fusion. If the structural variant calls were obtained from whole-exome sequencing (WES) data rather than WGS data, the filter no_genomic_support should be disabled, since WES has poor coverage in most regions of the genome, such that many structural variants are missed.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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646
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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647 Two file formats are accepted: a simple four-column format and the standard Variant Call Format (VCF). The format is detected automatically.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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648
1
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649 * In case of the simple format, the file must contain four columns separated by tabs. The first two columns contain the breakpoints of the structural variants in the format CONTIG:POSITION. The last two columns contain the orientation of the breakpoints. The accepted values are:
0
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650
1
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651 + downstream or +: the fusion partner is fused downstream of the breakpoint, i.e., at a coordinate higher than the breakpoint
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652 + upstream or -: the fusion partner is fused at a coordinate lower than the breakpoint
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653
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654 Example:
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655
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656 ::
0
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657
1
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658 =========== =========== =========== ===========
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659 5-prime 3-prime orientation orientation
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660 =========== =========== =========== ===========
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661 1:54420491 6:9248349 + -
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662 20:46703288 20:46734546 - +
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663 17:61499820 20:45133874 + +
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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664 3:190967119 7:77868317 - -
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665 =========== =========== =========== ===========
0
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666
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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667
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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668 * 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.
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669
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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670 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.
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671
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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672 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.
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673
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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674
9
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675 **OPTIONS**
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676
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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677 - Arriba: https://arriba.readthedocs.io/en/latest/command-line-options/#arriba
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678 - Visualization: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr
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679 - RNA STAR: https://arriba.readthedocs.io/en/latest/workflow/
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680
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681
6
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682 **OUTPUTS**
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683
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684 See: https://arriba.readthedocs.io/en/latest/output-files/
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685
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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686 - fusions.tsv
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687
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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688 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:
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689
1
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690 * 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 (.).
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691
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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692 * strand1(gene/fusion) and strand2(gene/fusion) : Each of these columns contains two values seperated by a slash. The strand before the slash reflects the strand of the gene according to the gene annotation supplied to Arriba via the parameter -g. If the breakpoint is in an intergenic region, the value is .. The value after the slash reflects the strand that is transcribed. This does not necessarily match the strand of the gene, namely when the sense strand of a gene serves as the template for transcription. Occassionally, the strand that is transcribed cannot be predicted reliably. In this case, Arriba indicates the lack of information as a dot (.). Arriba uses splice-patterns of the alignments to assign a read to the appropriate originating gene. If a strand-specific library was used, Arriba also evaluates the strandedness in ambiguous situations, for example, when none of the supporting reads overlaps a splice-site.
0
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693
1
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694 * 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.
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695
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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696 * 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.
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697
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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698 * 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.
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699
1
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700 * 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.
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701
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702 * discordant_mates : This column contains the number of pairs (fragments) of discordant mates (a.k.a. spanning reads or bridge reads) supporting the fusion.
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703
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704 * coverage1 and coverage2 : These two columns show the coverage near breakpoint1 and breakpoint2, respectively. The coverage is calculated as the number of fragments near the breakpoint on the side of the breakpoint that is retained in the fusion transcript. Note that the coverage calculation counts all fragments (even duplicates), whereas the columns split_reads1, split_reads2, and discordant_mates only count non-discarded reads. Fragments discarded due to being duplicates or other types of artifacts can be found in the column filters.
0
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705
1
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706 * 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.
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707
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708 * 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.
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709
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710 * tags : When a user-defined list of tags is provided via the parameter -t, this column is populated with the provided tag whenever a fusion matches the coordinates specified for the respective tag. When multiple tags match, they are separated by a comma.
0
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711
1
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712 * 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 (|).
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713
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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714 * closest_genomic_breakpoint1 and closest_genomic_breakpoint2 : When a matched whole-genome sequencing sample is available, one can feed structural variant calls obtained therefrom into Arriba (see parameter -d). Arriba then considers this information during fusion calling, which improves the overall accuracy. These two columns contain the coordinates of the genomic breakpoints which are closest to the transcriptomic breakpoints given in the columns breakpoint1 and breakpoint2. The values in parentheses are the distances between transcriptomic and genomic breakpoints.
0
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715
1
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716 * 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.
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717
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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718 * transcript_id1 and transcript_id2 : For both fused genes, Arriba determines the best matching isoform that is transcribed as part of the fusion. The isoform is selected by how well its annotated exons match the splice pattern of the supporting reads of a fusion.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
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719
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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720 * direction1 and direction2 : These columns indicate the orientation of the fusion. A value of downstream means that the partner is fused downstream of the breakpoint, i.e. at a coordinate higher than the breakpoint. A value of upstream means the partner is fused at a coordinate lower than the breakpoint. When the prediction of the strands or of the 5' gene fails, this information gives insight into which parts of the fused genes are retained in the fusion.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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721
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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722 * filters : This column lists the filters which removed one or more of the supporting reads. The section Internal algorithm describes all filters in detail. The number of filtered reads is given in parentheses after the name of the filter. The total number of supporting reads can be obtained by summing up the reads given in the columns split_reads1, split_reads2, discordant_mates, and filters. If a filter discarded the event as a whole (all reads), the number of filtered reads is not stated.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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diff changeset
723
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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724 * fusion_transcript : This column contains the fusion transcript sequence. The sequence is assembled from the supporting reads of the most highly expressed transcript. It represents the transcript isoform that is most likely expressed according to the splice patterns of the supporting reads. The column contains a dot (.), when the sequence could not be predicted. This is the case when the strands or the 5' end of the transcript could not be predicted reliably. The breakpoint is represented as a pipe symbol (|). When non-template bases are inserted between the fused genes, these bases are represented as lowercase letters between two pipes. Reference mismatches (SNPs or SNVs) are indicated as lowercase letters, insertions as bases between brackets ([ and ]), deleted bases as one or more dashes (-), introns as three underscores (___), and ambiguous positions, such as positions with diverse reference mismatches, are represented as ?. Missing information due to insufficient coverage is denoted as an ellipsis (...). If the switch -I is used, then an attempt is made to fill missing information with the assembly sequence. A sequence stretch that was taken from the assembly sequence rather than the supporting reads is wrapped in parentheses (( and )). In addition, when -I is used, the sequence is trimmed to the boundaries of the fused transcripts. The coordinate of the fusion breakpoint relative to the start of the transcript can thus easily be inferred by counting the bases from the beginning of the fusion transcript to the breakpoint character (|). In case the full sequence could be constructed from the combined information of supporting reads and assembly sequence, the start of the fusion transcript is marked by a caret sign (^) and the end by a dollar sign ($). If the full sequence could not be constructed, these signs are missing.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
jjohnson
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725
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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726 * peptide_sequence : This column contains the fusion peptide sequence. The sequence is translated from the fusion transcript given in the column fusion_transcript and determines the reading frame of the fused genes according to the transcript isoforms given in the columns transcript_id1 and transcript_id2. Translation starts at the start of the assembled fusion transcript or when the start codon is encountered in the 5' gene. Translation ends when either the end of the assembled fusion transcript is reached or when a stop codon is encountered. If the fusion transcript contains an ellipsis (...), the sequence beyond the ellipsis is trimmed before translation, because the reading frame cannot be determined reliably. The column contains a dot (.), when the transcript sequence could not be predicted or when the precise breakpoints are unknown due to lack of split reads or when the fusion transcript does not overlap any coding exons in the 5' gene or when no start codon could be found in the 5' gene or when there is a stop codon prior to the fusion junction (in which case the column reading_frame contains the value stop-codon). The breakpoint is represented as a pipe symbol (|). If a codon spans the breakpoint, the amino acid is placed on the side of the breakpoint where two of the three bases reside. Codons resulting from non-template bases are flanked by two pipes. Amino acids are written as lowercase characters in the following situations: non-silent SNVs/SNPs, insertions, frameshifts, codons spanning the breakpoint, non-coding regions (introns/intergenic regions/UTRs), and non-template bases. Codons which cannot be translated to amino acids, such as those having invalid characters, are represented as ?.
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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727
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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728 * read_identifiers : This column contains the names of the supporting reads separated by commas.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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729
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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730 - fusions.discarded.tsv
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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731
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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732 The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv.
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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733
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
jjohnson
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734
6
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
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735 **VISUALIZATION**
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736
7253b367c082 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit ea14642edb0816912a856281944eb5e8a37c11ea"
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737 See: https://arriba.readthedocs.io/en/latest/visualization/
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738
5
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739 - fusions.pdf
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9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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740
5
005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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741 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.
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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742
9
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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743 .. image:: draw-fusions-example.png
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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744 :width: 800
8c4c97fd0555 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
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745 :height: 467
0
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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746
1
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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747
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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748 .. _Arriba: https://arriba.readthedocs.io/en/latest/
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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749 .. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/
9f2665b32c45 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 933ae7dfba10b1b31c30a90216d76cdad6dda685"
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750 .. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/
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005b200c8841 "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
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751 .. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/
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752 .. _OPTIONS: https://arriba.readthedocs.io/en/latest/command-line-options/
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753
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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754 ]]></help>
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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755 <expand macro="citations" />
5ebf2354cc9b "planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 52c9f9825debe783339c13bd1da9a42b59747bd2"
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756 </tool>