annotate arriba.xml @ 3:f6b8b38636a4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078
author iuc
date Tue, 06 Dec 2022 10:38:51 +0000
parents add230dddd52
children 01ccd366690d
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a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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1 <tool id="arriba" name="Arriba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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2 <description>detect gene fusions from STAR aligned RNA-Seq data</description>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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3 <macros>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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4 <import>macros.xml</import>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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5 <xml name="fusion_actions">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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6 <actions>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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7 <action name="comment_lines" type="metadata" default="1" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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8 <action name="column_names" type="metadata" default="gene1,gene2,strand1(gene/fusion),strand2(gene/fusion),breakpoint1,breakpoint2,site1,site2,type,split_reads1,split_reads2,discordant_mates,coverage1,coverage2,confidence,reading_frame,tags,retained_protein_domains,closest_genomic_breakpoint1,closest_genomic_breakpoint2,gene_id1,gene_id2,transcript_id1,transcript_id2,direction1,direction2,filters,fusion_transcript,peptide_sequence,read_identifiers" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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9 </actions>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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10 </xml>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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11 <token name="@VIRAL_CONTIG@">([AN]C_([*]|\d+))</token>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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12 <token name="@GENOME_CONTIG@">((chr)?(\d|\d\d|X|Y|M(t)?))</token>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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13 </macros>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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14 <expand macro="requirements" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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15 <expand macro="version_command" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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16 <command detect_errors="exit_code"><![CDATA[
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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17 @GENOME_SOURCE@
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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18 @GTF_SOURCE@
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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19 #set $filter_list = []
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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20 #if $options.filters
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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21 #set $filter_list = $options.filters.split(',')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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22 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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23 #if $blacklist
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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24 #if $blacklist.is_of_type('tabular.gz')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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25 #set $blacklist_file = 'blacklist.tsv.gz'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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26 ln -sf '$blacklist' $blacklist_file &&
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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27 #else
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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28 #set $blacklist_file = $blacklist
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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29 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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30 #else
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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31 #if 'blacklist' not in $filter_list
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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32 #silent $filter_list.append('blacklist')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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33 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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34 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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35 #set $filters = ','.join($filter_list)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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36 #if $known_fusions
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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37 #if $known_fusions.is_of_type('tabular.gz')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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38 #set $known_fusions_file = 'known_fusions.tsv.gz'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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39 ln -sf '$known_fusions' $known_fusions_file &&
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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40 #else
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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41 #set $known_fusions_file = $known_fusions
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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42 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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43 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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44 #if $tags
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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45 #if $tags.is_of_type('tabular.gz')
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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46 #set $tags_file = 'tags.tsv.gz'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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47 ln -sf '$tags' $tags_file &&
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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48 #else
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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49 #set $tags_file = $tags
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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50 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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51 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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52 arriba
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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53 -x '$input'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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54 #if $chimeric
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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55 -c '$chimeric'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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56 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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57 -a '$genome_assembly'
1
4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
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58 -g 'genome.gtf'
0
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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59 #if $blacklist
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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60 -b '$blacklist_file'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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61 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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62 #if $filters
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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63 -f '$filters'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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64 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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65 #if $protein_domains
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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66 -p '$protein_domains'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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67 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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68 #if $known_fusions
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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69 -k '$known_fusions_file'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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70 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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71 #if $tags
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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72 -t '$tags_file'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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73 #end if
1
4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
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74 #if str($wgs_cond.use_wgs) == "yes"
4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
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75 -d '$wgs_cond.wgs'
2
add230dddd52 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 0856836a21e5cf745547dfcf0b9b98eb106e4952
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76 #if str($wgs_cond.max_genomic_breakpoint_distance)
1
4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
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77 -D $wgs_cond.max_genomic_breakpoint_distance
0
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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78 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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79 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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80 -o fusions.tsv
1
4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
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81 #if $output_fusions_discarded
0
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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82 -O fusions.discarded.tsv
1
4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
iuc
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83 #end if
4f1efcc055d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
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84 ## Arriba options
0
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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85 #if $options.gtf_features
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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86 -G '$options.gtf_features'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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87 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
88 #if $options.strandedness
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
89 -s $options.strandedness
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
90 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
91 #if $options.genome_contigs
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
92 -i '$options.genome_contigs'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
93 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
94 #if $options.viral_contigs
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
95 -v '$options.viral_contigs'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
96 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
97 #if str($options.max_evalue)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
98 -E $options.max_evalue
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
99 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
100 #if str($options.min_supporting_reads)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
101 -S $options.min_supporting_reads
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
102 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
103 #if str($options.max_mismappers)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
104 -m $options.max_mismappers
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
105 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
106 #if str($options.max_homolog_identity)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
107 -L $options.max_homolog_identity
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
108 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
109 #if str($options.homopolymer_length)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
110 -H $options.homopolymer_length
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
111 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
112 #if str($options.read_through_distance)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
113 -R $options.read_through_distance
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
114 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
115 #if str($options.min_anchor_length)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
116 -A $options.min_anchor_length
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
117 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
118 #if str($options.many_spliced_events)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
119 -M $options.many_spliced_events
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
120 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
121 #if str($options.max_kmer_content)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
122 -K $options.max_kmer_content
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
123 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
124 #if str($options.max_mismatch_pvalue)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
125 -V $options.max_mismatch_pvalue
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
126 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
127 #if str($options.fragment_length)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
128 -F $options.fragment_length
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
129 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
130 #if str($options.max_reads)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
131 -U $options.max_reads
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
132 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
133 #if $options.quantile
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
134 -Q $options.quantile
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
135 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
136 #if str($options.exonic_fraction)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
137 -e $options.exonic_fraction
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
138 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
139 #if str($options.top_n)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
140 -T $options.top_n
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
141 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
142 #if str($options.covered_fraction)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
143 -C $options.covered_fraction
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
144 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
145 #if str($options.max_itd_length)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
146 -l $options.max_itd_length
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
147 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
148 #if str($options.min_itd_allele_fraction)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
149 -z $options.min_itd_allele_fraction
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
150 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
151 #if str($options.min_itd_supporting_reads)
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
152 -Z $options.min_itd_supporting_reads
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
153 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
154 $options.duplicate_marking
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
155 $options.fill_discarded_columns
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
156 $options.fill_the_gaps
3
f6b8b38636a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078
iuc
parents: 2
diff changeset
157 #if $output_fusion_bams or str($visualization.do_viz) == "yes"
0
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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158 && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
159 && samtools index Aligned.sortedByCoord.out.bam
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
160 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
161 #if $output_fusions_vcf
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
162 && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
163 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
164 #if $output_fusion_bams
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
165 && mkdir fusion_bams
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
166 && extract_fusion-supporting_alignments.sh fusions.tsv Aligned.sortedByCoord.out.bam 'fusion_bams/fusion'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
167 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
168 #if str($visualization.do_viz) == "yes"
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
169 #set $fusions = 'fusions.tsv'
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
170 && @DRAW_FUSIONS@
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
171 #end if
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
172 ]]></command>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
173 <inputs>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
174 <param name="input" argument="-x" type="data" format="sam,bam,cram" label="STAR Aligned.out.sam">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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175 <help><![CDATA[ recommended STAR options: --chimSegmentMin 10 --chimOutType WithinBAM ]]></help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
176 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
177 <param name="chimeric" argument="-c" type="data" format="sam,bam,cram" optional="true" label="STAR Chimeric.out.sam">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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178 <help><![CDATA[ only required, if STAR was run with the parameter '--chimOutType SeparateSAMold' ]]></help>
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179 </param>
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180 <expand macro="genome_source" />
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181 <expand macro="gtf_source" />
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182 <param name="blacklist" argument="-b" type="data" format="tabular,tabular.gz" optional="true" label="File containing blacklisted ranges."/>
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183 <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/>
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184 <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz" optional="true" label="File containing known fusions">
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185 <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
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186 </param>
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187 <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."
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188 help="This can be the known fusions if that input has a third column with a name"/>
1
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189 <conditional name="wgs_cond">
0
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190 <param name="use_wgs" type="select" label="Use whole-genome sequencing data">
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191 <option value="no">no</option>
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192 <option value="yes">Yes</option>
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193 </param>
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194 <when value="yes">
1
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195 <param name="wgs" argument="-d" type="data" format="tabular,vcf" label="whole-genome sequencing structural variant data"
0
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196 help="These coordinates serve to increase sensitivity towards weakly expressed fusions and to eliminate fusions with low evidence."/>
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197 <param name="max_genomic_breakpoint_distance" argument="-D" type="integer" value="100000" min="0" label="Max genomic breakpoint distance"
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198 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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199 </when>
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200 <when value="no"/>
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201 </conditional>
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202 <section name="options" expanded="false" title="Arriba Options">
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203 <param name="gtf_features" argument="-G" type="text" value="" optional="true" label="Names of features in the GTF annotation file">
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204 <help>Commma or SPACE separated list, default: gene_name=gene_name|gene_id gene_id=gene_id transcript_id=transcript_id feature_exon=exon feature_CDS=CDS</help>
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205 <validator type="regex" message="">^(gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=\w+(|\w+)?([ ,](gene_name|gene_id|transcript_id|feature_exon|feature_CDS)=\w+(|\w+)?)*$</validator>
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206 </param>
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207 <param name="strandedness" argument="-s" type="select" optional="true" label="Whether a strand-specific protocol was used for library preparation">
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208 <help>When unstranded data is processed, the strand can sometimes be inferred from splice-patterns. But in unclear situations, stranded data helps resolve ambiguities.</help>
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209 <option value="auto">auto</option>
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210 <option value="yes">yes</option>
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211 <option value="no">no</option>
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212 <option value="reverse">reverse</option>
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213 </param>
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214 <param name="genome_contigs" argument="-i" type="text" value="" optional="true" label="Comma/space-separated list of interesting contigs">
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215 <help>Comma-/space-separated list of interesting contigs.
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216 Fusions between genes on other contigs are ignored. Contigs can be specified with or without the prefix "chr".
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217 Asterisks (*) are treated as wild-cards.
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218 Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*
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219 </help>
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220 <validator type="regex" message="not a valid contig name">^((@GENOME_CONTIG@|@VIRAL_CONTIG@)([,\s]\s*(*@GENOME_CONTIG@|@VIRAL_CONTIG@))*)*</validator>
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221 </param>
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222 <param name="viral_contigs" argument="-v" type="text" value="" optional="true" label="Comma/space-separated list of viral contigs">
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223 <help>Comma-/space-separated list of viral contigs for reporting of viral integration sites.
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224 Asterisks (*) are treated as wild-cards.
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225 Default: AC_* NC_*
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226 </help>
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227 <validator type="regex" message="not a valid contig name">^(@VIRAL_CONTIG@([,\s]\s*@VIRAL_CONTIG@)*)*$</validator>
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228 </param>
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229 <param name="filters" argument="-f" type="select" optional="true" multiple="true" label="Disable filters">
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230 <help>By default all filters are enabled.</help>
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231 <option value="top_expressed_viral_contigs">top_expressed_viral_contigs</option>
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232 <option value="viral_contigs">viral_contigs</option>
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233 <option value="low_coverage_viral_contigs">low_coverage_viral_contigs</option>
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234 <option value="uninteresting_contigs">uninteresting_contigs</option>
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235 <option value="no_genomic_support">no_genomic_support</option>
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236 <option value="short_anchor">short_anchor</option>
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237 <option value="select_best">select_best</option>
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238 <option value="many_spliced">many_spliced</option>
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239 <option value="long_gap">long_gap</option>
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240 <option value="merge_adjacent">merge_adjacent</option>
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241 <option value="hairpin">hairpin</option>
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242 <option value="small_insert_size">small_insert_size</option>
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243 <option value="same_gene">same_gene</option>
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244 <option value="genomic_support">genomic_support</option>
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245 <option value="read_through">read_through</option>
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246 <option value="no_coverage">no_coverage</option>
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247 <option value="mismatches">mismatches</option>
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248 <option value="homopolymer">homopolymer</option>
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249 <option value="low_entropy">low_entropy</option>
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250 <option value="multimappers">multimappers</option>
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251 <option value="inconsistently_clipped">inconsistently_clipped</option>
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252 <option value="duplicates">duplicates</option>
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253 <option value="homologs">homologs</option>
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254 <option value="blacklist">blacklist</option>
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255 <option value="mismappers">mismappers</option>
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256 <option value="spliced">spliced</option>
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257 <option value="relative_support">relative_support</option>
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258 <option value="min_support">min_support</option>
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259 <option value="known_fusions">known_fusions</option>
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260 <option value="end_to_end">end_to_end</option>
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261 <option value="non_coding_neighbors">non_coding_neighbors</option>
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262 <option value="isoforms">isoforms</option>
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263 <option value="intronic">intronic</option>
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264 <option value="in_vitro">in_vitro</option>
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265 <option value="intragenic_exonic">intragenic_exonic</option>
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266 <option value="internal_tandem_duplication">internal_tandem_duplication</option>
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267 </param>
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268
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269 <param name="max_evalue" argument="-E" type="float" value="" min="0" optional="true" label="Max e-value threshold">
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270 <help>Arriba estimates the number of fusions with a given number of supporting
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271 reads which one would expect to see by random chance. If the expected number
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272 of fusions (e-value) is higher than this threshold, the fusion is
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273 discarded by the 'relative_support' filter. Note: Increasing this
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274 threshold can dramatically increase the number of false positives and may
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275 increase the runtime of resource-intensive steps. Fractional values are possible.
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276 Default: 0.300000
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277 </help>
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278 </param>
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279
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280 <param name="min_supporting_reads" argument="-S" type="integer" value="" min="1" optional="true" label="Min supporting reads">
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281 <help>discard all fusions with fewer than this many supporting reads (split reads and discordant mates combined).
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282 Default: 2
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283 </help>
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284 </param>
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285 <param name="max_mismappers" argument="-m" type="float" value="" min="0." max="1.0" optional="true" label="Max mismappers threshold">
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286 <help>When more than this fraction of supporting reads turns out to be mismappers,
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287 the 'mismappers' filter discards the fusion.
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288 Default: 0.800000
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289 </help>
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290 </param>
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291 <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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292 <help>Genes with more than the given fraction of sequence identity are
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293 considered homologs and removed by the 'homologs' filter.
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294 Default: 0.300000
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295 </help>
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296 </param>
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297 <param name="homopolymer_length" argument="-H" type="integer" value="" min="1" optional="true" label="Homopolymer length">
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298 <help>The 'homopolymer' filter removes breakpoints adjacent to homopolymers of the given length or more.
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299 Default: 6
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300 </help>
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301 </param>
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302 <param name="read_through_distance" argument="-R" type="integer" value="" min="1" optional="true" label="Read-through distance">
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303 <help>The 'read_through' filter removes read-through fusions
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304 where the breakpoints are less than the given distance away from each other.
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305 Default: 10000
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306 </help>
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307 </param>
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308 <param name="min_anchor_length" argument="-A" type="integer" value="" min="1" optional="true" label="Min anchor length">
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309 <help>Alignment artifacts are often characterized by split reads coming
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310 from only one gene and no discordant mates. Moreover, the split
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311 reads only align to a short stretch in one of the genes. The
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312 'short_anchor' filter removes these fusions. This parameter sets
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313 the threshold in bp for what the filter considers short.
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314 Default: 23
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315 </help>
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316 </param>
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317 <param name="many_spliced_events" argument="-M" type="integer" value="" min="1" optional="true" label="Many spliced events">
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318 <help>The 'many_spliced' filter recovers fusions between genes that
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319 have at least this many spliced breakpoints.
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320 Default: 4
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321 </help>
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322 </param>
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323 <param name="max_kmer_content" argument="-K" type="float" value="" min="0." max="1.0" optional="true" label="Max kmer content">
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324 <help>The 'low_entropy' filter removes reads with repetitive 3-mers. If
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325 the 3-mers make up more than the given fraction of the sequence, then
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326 the read is discarded.
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327 Default: 0.600000
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328 </help>
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329 </param>
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330
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331 <param name="max_mismatch_pvalue" argument="-V" type="float" value="" min="0." max="1." optional="true" label="Max mismatchrpvalue threahold">
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332 <help>The 'mismatches' filter uses a binomial model to calculate a
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333 p-value for observing a given number of mismatches in a read.
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334 If the number of mismatches is too high, the read is discarded.
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335 Default: 0.010000
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336 </help>
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337 </param>
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338
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339 <param name="fragment_length" argument="-F" type="integer" value="" min="1" optional="true" label="Single-end fragment length">
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340 <help>When paired-end data is given, the fragment length is estimated
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341 automatically and this parameter has no effect. But when single-end
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342 data is given, the mean fragment length should be specified to
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343 effectively filter fusions that arise from hairpin structures.
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344 Default: 200
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345 </help>
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346 </param>
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347 <param name="max_reads" argument="-U" type="integer" value="" min="1" optional="true" label="Max reads">
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diff changeset
348 <help>Subsample fusions with more than the given number of supporting reads. This
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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349 improves performance without compromising sensitivity, as long as the
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
350 threshold is high. Counting of supporting reads beyond the threshold is
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
351 inaccurate, obviously.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
352 Default: 300
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
353 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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354 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
355 <param name="quantile" argument="-Q" type="float" value="" min="0." max="1.0" optional="true" label="Quantile">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
356 <help>Highly expressed genes are prone to produce artifacts during library preparation.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
357 Genes with an expression above the given quantile are eligible for filtering by the 'in_vitro' filter.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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358 Default: 0.998000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
359 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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360 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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361 <param name="exonic_fraction" argument="-e" type="float" value="" min="0." max="1.0" optional="true" label="Exonic fraction">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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362 <help>The breakpoints of false-positive predictions of intragenic events
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
363 are often both in exons. True predictions are more likely to have at
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
364 least one breakpoint in an intron, because introns are larger.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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365 If the fraction of exonic sequence between two breakpoints is smaller than
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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366 the given fraction, the 'intragenic_exonic' filter discards the event.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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367 Default: 0.330000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
368 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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369 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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370
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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371 <param name="top_n" argument="-T" type="integer" value="" min="1" optional="true" label="top N viral contigs">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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372 <help>Only report viral integration sites of the top N most highly expressed viral contigs.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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373 Default: 5
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
374 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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375 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
376 <param name="covered_fraction" argument="-C" type="float" value="" min="0." max="1.0" optional="true" label="Covered fraction">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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377 <help>Ignore virally associated events if the virus is not fully expressed,
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
378 i.e., less than the given fraction of the viral contig is transcribed.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
379 Default: 0.050000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
380 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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381 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
382 <param name="max_itd_length" argument="-l" type="integer" value="" min="1" optional="true" label="Maximum length of internal tandem duplications">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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383 <help>Note: Increasing this value beyond the default can impair performance and lead to many false positives.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
384 Default: 100
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
385 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
386 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
387 <param name="min_itd_allele_fraction" argument="-z" type="float" value="" min="0." max="1.0" optional="true" label="Required fraction of supporting reads to report an internal tandem duplication">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
388 <help> Default: 0.070000
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
389 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
390 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
391 <param name="min_itd_supporting_reads" argument="-Z" type="integer" value="" min="1" optional="true" label="Required number of supporting reads to report an internal tandem duplication">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
392 <help> Default: 10
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
393 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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394 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
395 <param name="duplicate_marking" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Use aligners duplicate marking">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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396 <help>Instead of performing duplicate marking itself, Arriba relies on duplicate marking by a
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
397 preceding program using the BAM_FDUP flag. This makes sense when unique molecular
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
398 identifiers (UMI) are used.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
399 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
400 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
401 <param name="fill_discarded_columns" argument="-X" type="boolean" truevalue="-X" falsevalue="" checked="false" label="Fill all fusion.discarded.tsv columns">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
402 <help>To reduce the runtime and file size, by default, the columns 'fusion_transcript',
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
403 'peptide_sequence', and 'read_identifiers' are left empty in the file containing
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
404 discarded fusion candidates (see parameter -O). When this flag is set, this extra
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
405 information is reported in the discarded fusions file.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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406 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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407 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
408 <param name="fill_the_gaps" argument="-I" type="boolean" truevalue="-I" falsevalue="" checked="false" label="Fill fusion transcript gaps from the assembly">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
409 <help>If assembly of the fusion transcript sequence from the supporting reads is incomplete
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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410 (denoted as '...'), fill the gaps using the assembly sequence wherever possible.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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411 </help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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412 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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413 </section>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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414 <param name="output_fusions_discarded" argument="-O" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.discarded.tsv"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
415 <param name="output_fusions_vcf" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.vcf"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
416 <param name="output_fusion_bams" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output fusion BAMs"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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417 <conditional name="visualization">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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418 <param name="do_viz" type="select" label="Generate visualization">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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419 <option value="yes">Yes</option>
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420 <option value="no">no</option>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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421 </param>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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422 <when value="yes">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
423 <expand macro="visualization_options" />
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424 </when>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
425 <when value="no"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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426 </conditional>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
427 </inputs>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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428 <outputs>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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429 <data name="fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
430 <expand macro="fusion_actions" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
431 </data>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
432
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
433 <data name="discarded_fusions_tsv" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
434 <filter> output_fusions_discarded == True</filter>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
435 <expand macro="fusion_actions" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
436 </data>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
437 <data name="fusions_vcf" format="vcf" label="${tool.name} on ${on_string}: fusions.vcf" from_work_dir="fusions.vcf">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
438 <filter> output_fusions_vcf == True</filter>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
439 </data>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
440 <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
441 <discover_datasets pattern="(?P&lt;name&gt;fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
442 <filter>output_fusion_bams == True</filter>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
443 </collection>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
444 <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
445 <filter>visualization['do_viz'] == "yes"</filter>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
446 </data>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
447 </outputs>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
448 <tests>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
449 <!-- Test 1 - From exisitng BAM -->
3
f6b8b38636a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078
iuc
parents: 2
diff changeset
450 <test expect_num_outputs="3">
0
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
451 <param name="input" ftype="sam" value="Aligned.out.sam"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
452 <conditional name="genome">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
453 <param name="genome_source" value="history"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
454 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
455 </conditional>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
456 <conditional name="genome_gtf">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
457 <param name="gtf_source" value="history"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
458 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
459 </conditional>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
460 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
461 <conditional name="visualization">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
462 <param name="do_viz" value="no"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
463 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
464 </conditional>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
465 <output name="fusions_tsv">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
466 <assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
467 <has_text_matching expression="BCR\tABL1"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
468 </assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
469 </output>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
470 </test>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
471 <!-- Test 2 - From exisitng BAM with protein_domains and visualization -->
3
f6b8b38636a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit cd9d5f90669555dc06b2467043c01846cd8c4078
iuc
parents: 2
diff changeset
472 <test expect_num_outputs="4">
0
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
473 <param name="input" ftype="sam" value="Aligned.out.sam"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
474 <conditional name="genome">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
475 <param name="genome_source" value="history"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
476 <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
477 </conditional>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
478 <conditional name="genome_gtf">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
479 <param name="gtf_source" value="history"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
480 <param name="annotation" ftype="gtf" value="genome.gtf.gz"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
481 </conditional>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
482 <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
483 <conditional name="visualization">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
484 <param name="do_viz" value="yes"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
485 <param name="cytobands" ftype="tabular" value="cytobands.tsv"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
486 </conditional>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
487 <output name="fusions_tsv">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
488 <assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
489 <has_text_matching expression="BCR\tABL1"/>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
490 </assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
491 </output>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
492 <output name="fusions_pdf">
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
493 <assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
494 <has_size value= "64000" delta="5000" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
495 </assert_contents>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
496 </output>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
497 </test>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
498
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
499 </tests>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
500 <help><![CDATA[
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
501 **Arriba**
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
502
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
503
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
504 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
505 It is based on chimeric alignments found by the STAR RNA-Seq aligner.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
506
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
507
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
508 **INPUTS**
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
509
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
510 See: https://arriba.readthedocs.io/en/latest/input-files/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
511
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
512 - Alignments
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
513
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
514 Arriba takes the main output file of STAR (Aligned.out.bam) as input (parameter -x). If STAR was run with the parameter --chimOutType WithinBAM, then this file contains all the information needed by Arriba to find fusions. When STAR was run with the parameter --chimOutType SeparateSAMold, the main output file lacks chimeric alignments. Instead, STAR writes them to a separate output file named Chimeric.out.sam. In this case, the file needs to be passed to Arriba via the parameter -c in addition to the main output file Aligned.out.bam.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
515
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
516 STAR index create recommended parameter value:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
517
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
518 * --sjdbOverhang 250
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
519
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
520
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
521 STAR recommended parameter values ::
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
522
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
523 * --outSAMunmapped Within
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524 * --outFilterMultimapNmax 50
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525 * --peOverlapNbasesMin 10
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526 * --alignSplicedMateMapLminOverLmate 0.5
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527 * --alignSJstitchMismatchNmax 5 -1 5 5
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528 * --chimSegmentMin 10
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529 * --chimOutType WithinBAM HardClip
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530 * --chimJunctionOverhangMin 10
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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531 * --chimScoreDropMax 30
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532 * --chimScoreJunctionNonGTAG 0
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533 * --chimScoreSeparation 1
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534 * --chimSegmentReadGapMax 3
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535 * --chimMultimapNmax 50
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536
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537
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538 Arriba extracts three types of reads from the alignment file(s):
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539
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540 * Split-reads, i.e., reads composed of segments which map in a non-linear way. STAR stores such reads as supplementary alignments.
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541 * Discordant mates, i.e., paired-end reads which originate from the same fragment but which align in a non-linear way.
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542 * Alignments which cross the boundaries of annotated genes, because these alignments might arise from focal deletions. In RNA-Seq data deletions of up to several hundred kb are hard to distinguish from splicing. They are represented identically as gapped alignments, because the sizes of many introns are in fact of this order of magnitude. STAR applies a rather arbitrary measure to decide whether a gapped alignment arises from splicing or from a genomic deletion: The parameter --alignIntronMax determines what gap size is still assumed to be a splicing event and introns are used to represent these gaps. Only gaps larger than this limit are classified as potential evidence for genomic deletions and are stored as chimeric alignments. Most STAR-based fusion detection tools only consider chimeric alignments as evidence for gene fusions and are blind to focal deletions, hence. As a workaround, these tools recommend reducing the value of the parameter --alignIntronMax. But this impairs the quality of alignment, because it reduces the scope that STAR searches to find a spliced alignment. To avoid compromising the quality of alignment for the sake of fusion detection, the only solution would be to run STAR twice - once with settings optimized for regular alignment and once for fusion detection. This would double the runtime. In contrast, Arriba does not require to reduce the maximum intron size. It employs a more sensible criterion to distinguish splicing from deletions: Arriba considers all those reads as potential evidence for deletions that span the boundary of annotated genes.
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543
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544 The alignment files can be in SAM, BAM, and CRAM format. They need not be sorted for Arriba to accept them, but doing so comes with benefits: Often, this reduces the file size. And more importantly, the supporting reads of a fusion can be inspected visually using a genome browser like IGV, which typically requires BAM files to be sorted by coordinate.
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545
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546 Single-end and paired-end data and even mixtures are supported. Arriba automatically determines the data type on a read-by-read basis using the flag BAM_FPAIRED.
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547
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548
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549 - Assembly
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550
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551 Arriba takes the assembly as input (parameter -a) to find mismatches between the chimeric reads and the reference genome, as well as to find alignment artifacts and homologous genes.
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552
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553 The script download_references.sh can be used to download the assembly. The available assemblies are listed when the script is run without parameters. The user is not restricted to these assemblies, however. Any assembly can be used as long as its coordinates are compatible with one of the supported assemblies (hg19/hs37d5/GRCh37 or hg38/GRCh38 or mm10/GRCm38).
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554
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555 The assembly must be provided in FastA format and may be gzip-compressed. An index with the file extension .fai must exist only if CRAM files are processed.
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556
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557 - Annotation
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558
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559 The gene annotation (parameter -g) is used for multiple purposes:
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560
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561 annotation of breakpoints with genes
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562 increased sensitivity for breakpoints at splice-sites
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563 calculation of transcriptomic distances
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564 determining the putative orientation of fused genes (i.e., 5' and 3' end)
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565 GENCODE annotation is recommended over RefSeq annotation, because the former has a more comprehensive annotation of transcripts and splice-sites, which boosts the sensitivity. The file must be provided in GTF format and may be gzip-compressed. It does not need to be sorted.
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566
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567 The script download_references.sh can be used to download the annotation. The available annotation files are listed when the script is run without parameters. The user is not restricted to these annotation files, however. Any annotation can be used as long as its coordinates are compatible with one of the supported assemblies (hg19/hs37d5/GRCh37 or hg38/GRCh38 or mm10/GRCm38).
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568
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569
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570 - Blacklist
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571
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572 It is strongly advised to run Arriba with a blacklist (parameter -b). Otherwise, the false positive rate increases by an order of magnitude. For this reason, using Arriba with assemblies or organisms which are not officially supported is not recommended. At the moment, the supported assemblies are: hg19/hs37d5/GRCh37, hg38/GRCh38, and mm10/GRCm38 (as well as any other assemblies that have compatible coordinates). The blacklists are contained in the release tarballs of Arriba.
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573
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574 The blacklist removes recurrent alignment artifacts and transcripts which are present in healthy tissue. This helps eliminate frequently observed transcripts, such as read-through fusions between neighboring genes, circular RNAs and other non-canonically spliced transcripts. It was trained on RNA-Seq samples from the Human Protein Atlas, the Illumina Human BodyMap2 , the ENCODE project , the Roadmap Epigenomics project, and the NCT MASTER cohort, a heterogeneous cohort of cancer samples, from which highly recurrent artifacts were identified.
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575
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576 Blacklists for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/blacklist_*.
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577
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578 The blacklist is a tab-separated file with two columns and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions between which events are ignored. A region can be:
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579 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). If CONTIG ends on an asterisk (*), the contig with the closest matching name is chosen.
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580 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
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581 * the name of a gene given in the provided annotation.
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582
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583 In addition, special keywords are allowed for the second column:
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584 * any: Discard all events if one of the breakpoints matches the given region.
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585 * split_read_donor: Discard fusions only supported by split reads, if all of them have their anchor in the gene given in the first column. This filter is useful for highly mutable loci, which frequently trigger clipped alignments, such as the immunoglobulin loci or the T-cell receptor loci.
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586 * split_read_acceptor: Discard events only supported by split reads, if all of them have their clipped segment in the given region.
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587 * split_read_any: Discard events only supported by split reads, regardless of where the anchor is.
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588 * discordant_mates: Discard fusions, if they are only supported by discordant mates (no split reads).
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589 * low_support: Discard events, which have few supporting reads relative to expression (as determined by the filter relative_support), even if there is other evidence that the fusion might be a true positive, nonetheless. This keyword effectively prevents recovery of speculative events by filters such as spliced or many_spliced.
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590 * filter_spliced: This keyword prevents the filter spliced from being applied to a given region. It is triggered under the same circumstances as the keyword low_support, but additionally requires that the breakpoints be at splice-sites for the event to be discarded. Some breakpoints produce recurrent artifacts, but the second breakpoint is always a different one, such that the pair of breakpoints is not recurrent and cannot be blacklisted. Often, such breakpoints are at splice-sites and the filter spliced tends to recover them. This keyword prevents the filter from doing so.
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591 * not_both_spliced: This keyword discards events, unless both breakpoints are at splice-sites. This is a strict blacklist criterion, which makes sense to apply to genes which are prone to produce artifacts, because they are highly expressed, for example hemoglobins, collagens, or ribosomal genes.
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592 * read_through: This keyword discards events, if they could arise from read-through transcription, i.e., the supporting reads are oriented like a deletion and are at most 400 kb apart.
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593
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594
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595 - Known fusions
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596
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597 Arriba can be instructed to be particularly sensitive towards events between certain gene pairs by supplying a list of gene pairs (parameter -k). A number of filters are not applied to these gene pairs. This is useful to improve the detection rate of expected or highly relevant events, such as recurrent fusions. Occassionally, this leads to false positive calls. But if high sensitivity is more important than specificity, this might be acceptable. Events which would be discarded by a filter and were recovered due to being listed in the known fusions list are usually assigned a low confidence.
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598
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599 Known fusions files for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/known_fusions_*.
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diff changeset
600
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
601 The file has two columns separated by a tab and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions to which very sensitive filtering thresholds are applied. A region can be:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
602
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
603 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754). If CONTIG ends on an asterisk (*), the contig with the closest matching name is chosen.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
604 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
605 * the name of a gene given in the provided annotation.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
606
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
607 The order of the given regions is important. The region given in the first column is assumed to denote the 5' end of the fusion and the region in the second column to be the 3' end. If Arriba cannot determine with confidence which gene constitutes the 5' and which the 3' end of a fusion prediction, then the order is ignored and the prediction is rescued in both cases.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
608
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
parents:
diff changeset
609
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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diff changeset
610 - Tags
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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611
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
612 Arriba can be supplied with a list of user-defined tags using the parameter -t. Whenever a fusion prediction matches the selection criteria for a tag, the column tags is populated with the respective tag. This feature is useful to annotate known oncogenic fusions, for example.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
613
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
614 The known fusions file shipped with the download package of Arriba can be used for both known fusions and tags. It is constructed in a way that it can be passed as arguments to the parameters -k and -t alike. The former only uses the first two columns, the latter uses all three columns. If a user wants to separate filtering of known fusions and tagging of interesting fusions, different files may be used, however.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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615
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
616 The file has three columns separated by a tab and may optionally be gzip-compressed. Lines starting with a hash (#) are treated as comments. Each line represents a pair of regions to be annotated. The first two columns specify the regions to be annotated; the third column the tag that is used for annotation. Some special characters in the tag are replaced with underscores (_) in Arriba's output file. A region can be:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
617
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
618 * a 1-based coordinate in the format CONTIG:POSITION, optionally prefixed with the strand (example: +9:56743754).
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
619 * a range in the format CONTIG:START-END, optionally prefixed with a strand (example: 9:1000000-1100000).
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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620 * the name of a gene given in the provided annotation.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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621
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
622 The order of the given regions is important. The region given in the first column is assumed to denote the 5' end of the fusion and the region in the second column to be the 3' end.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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623
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
624 - Protein domains
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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625
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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626 Protein domain annotation can be passed to Arriba via the parameter -p. The column retained_protein_domains of Arriba's output file is then populated accordingly.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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627
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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628 Protein domain annotation files for all supported assemblies are shipped with the download package of Arriba. They can be found in the package as database/protein_domains_*.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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629
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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630 The file must be in GFF3 format and may optionally be gzip-compressed. The ninth column must at least contain the following attributes:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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631 * Name=PROTEIN_DOMAIN_NAME;
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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632 * gene_id=GENE_ID;
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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633 * gene_name=GENE_NAME
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634
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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635 The attribute Name is reported in the column retained_protein_domains of Arriba's output file. Some special characters in the name are replaced with underscores (_). The columns gene_id and gene_name are used to match the protein domains to the genes given in the gene annotation. If a match cannot be found, Arriba cannot determine the retained protein domains of the respective gene and a warning is issued. There may be many warnings if RefSeq annotation is used, because the protein domains file distributed with Arriba uses ENSEMBL gene names/IDs.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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636
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637 - Structural variant calls from WGS
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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638
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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639 If whole-genome sequencing (WGS) data is available, the sensitivity and specificity of Arriba can be improved by passing a list of structural variants detected from WGS to Arriba via the parameter -d. This has the following effects:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
640
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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641 Certain filters are overruled or run with extra sensitive settings, when an event is confirmed by WGS data.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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642 To reduce the false positive rate, Arriba does not report low-confidence events unless they can be matched with a structural variant found in the WGS data.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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643 Both of these behaviors can be disabled by disabling the filters genomic_support and no_genomic_support, respectively. Providing Arriba with a list of structural variant calls then does not influence the calls, but it still has the benefit of filling the columns closest_genomic_breakpoint1 and closest_genomic_breakpoint2 with the breakpoints of the structural variant which is closest to a fusion. If the structural variant calls were obtained from whole-exome sequencing (WES) data rather than WGS data, the filter no_genomic_support should be disabled, since WES has poor coverage in most regions of the genome, such that many structural variants are missed.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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644
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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645 Two file formats are accepted: a simple four-column format and the standard Variant Call Format (VCF). The format is detected automatically.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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646
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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647 * In case of the simple format, the file must contain four columns separated by tabs. The first two columns contain the breakpoints of the structural variants in the format CONTIG:POSITION. The last two columns contain the orientation of the breakpoints. The accepted values are:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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648
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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649 + downstream or +: the fusion partner is fused downstream of the breakpoint, i.e., at a coordinate higher than the breakpoint
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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650 + upstream or -: the fusion partner is fused at a coordinate lower than the breakpoint
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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651
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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652 Example:
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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653
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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654 ::
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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655
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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656 =========== =========== =========== ===========
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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657 5-prime 3-prime orientation orientation
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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658 =========== =========== =========== ===========
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659 1:54420491 6:9248349 + -
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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660 20:46703288 20:46734546 - +
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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661 17:61499820 20:45133874 + +
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662 3:190967119 7:77868317 - -
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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663 =========== =========== =========== ===========
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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664
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665
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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666 * In case of the Variant Call Format, the file must comply with the VCF specification for structural variants. In particular, Arriba requires that the SVTYPE field be present in the INFO column and specify one of the four values BND, DEL, DUP, INV. In addition, for all SVTYPEs other than BND, the END field must be present and specify the second breakpoint of the structural variant. Structural variants with single breakends are silently ignored.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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667
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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668 Arriba checks if the orientation of the structural variant matches that of a fusion detected in the RNA-Seq data. If, for example, Arriba predicts the 5' end of a gene to be retained in a fusion, then a structural variant is expected to confirm this, or else the variant is not considered to be related.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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669
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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670 NOTE: Arriba was designed for alignments from RNA-Seq data. It should not be run on WGS data directly. Many assumptions made by Arriba about the data (statistical models, blacklist, etc.) only apply to RNA-Seq data and are not valid for DNA-Seq data. For such data, a structural variant calling algorithm should be used and the results should be passed to Arriba.
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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671
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672
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673 **OPTIONS**
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674
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675 - Arriba: https://arriba.readthedocs.io/en/latest/command-line-options/#arriba
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676 - Visualization: https://arriba.readthedocs.io/en/latest/command-line-options/#draw_fusionsr
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677 - RNA STAR: https://arriba.readthedocs.io/en/latest/workflow/
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678
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679
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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diff changeset
680 **OUTPUTS**
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681
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682 See: https://arriba.readthedocs.io/en/latest/output-files/
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683
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684 - fusions.tsv
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685
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686 The file fusions.tsv (as specified by the parameter -o) contains fusions which pass all of Arriba's filters. It should be highly enriched for true predictions. The predictions are listed from highest to lowest confidence. The following paragraphs describe the columns in detail:
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687
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688 * gene1 and gene2 : gene1 contains the gene which makes up the 5' end of the transcript and gene2 the gene which makes up the 3' end. The order is predicted on the basis of the strands that the supporting reads map to, how the reads are oriented, and splice patterns. Both columns may contain the same gene, if the event is intragenic. If a breakpoint is in an intergenic region, Arriba lists the closest genes upstream and downstream from the breakpoint, separated by a comma. The numbers in parentheses after the closest genes state the distance to the genes. If no genes are annotated for a contig (e.g., for viral genomes), the column contains a dot (.).
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689
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690 * strand1(gene/fusion) and strand2(gene/fusion) : Each of these columns contains two values seperated by a slash. The strand before the slash reflects the strand of the gene according to the gene annotation supplied to Arriba via the parameter -g. If the breakpoint is in an intergenic region, the value is .. The value after the slash reflects the strand that is transcribed. This does not necessarily match the strand of the gene, namely when the sense strand of a gene serves as the template for transcription. Occassionally, the strand that is transcribed cannot be predicted reliably. In this case, Arriba indicates the lack of information as a dot (.). Arriba uses splice-patterns of the alignments to assign a read to the appropriate originating gene. If a strand-specific library was used, Arriba also evaluates the strandedness in ambiguous situations, for example, when none of the supporting reads overlaps a splice-site.
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691
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692 * breakpoint1 and breakpoint2 : The columns contain the coordinates of the breakpoints in gene1 and gene2, respectively. If an event is not supported by any split reads but only by discordant mates, the coordinates given here are those of the discordant mates which are closest to the true but unknown breakpoint.
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693
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694 * site1 and site2 : These columns add information about the location of the breakpoints. Possible values are: 5' UTR, 3' UTR, UTR (overlapping with a 5' UTR as well as a 3' UTR), CDS (coding sequence), exon, intron, and intergenic. The keyword exon is used for non-coding genes or for ambiguous situations where the breakpoint overlaps with both a coding exon and a UTR. If the breakpoint coincides with an exon boundary, the additional keyword splice-site is appended.
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695
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696 * type : Based on the orientation of the supporting reads and the coordinates of breakpoints, the type of event can be inferred. Possible values are: translocation (between different chromosomes), duplication, inversion, and deletion. If genes are fused head-to-head or tail-to-tail, this is indicated as 5'-5' or 3'-3' respectively. Genes fused in such an orientation cannot yield a chimeric protein, since one of the genes is transcribed from the wrong strand. This type of event is equivalent to the truncation of the genes. The following types of events are flagged with an extra keyword, because they are frequent types of false positives and/or it is not clear if they are somatic or germline variants: Deletions with a size in the range of introns (<400kb) are flagged as read-through, because there is a high chance that the fusion arises from read-through transcription rather than an underlying genomic deletion. Intragenic duplications with both breakpoints at splice-sites are flagged as non-canonical-splicing, because the supporting reads might originate from circular RNAs, which are very abundant even in normal tissue, but manifest as duplications in RNA-Seq data. Internal tandem duplications are flagged as ITD. It is not always clear whether the ITDs observable in RNA-Seq data are somatic or germline variants, because ITDs are abundant in the germline and germline variants cannot be filtered effectively due to lack of a normal control.
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697
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698 * split_reads1 and split_reads2 : The number of supporting split fragments with an anchor in gene1 or gene2, respectively, is given in these columns. The gene to which the longer segment of the split read aligns is defined as the anchor.
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699
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700 * discordant_mates : This column contains the number of pairs (fragments) of discordant mates (a.k.a. spanning reads or bridge reads) supporting the fusion.
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701
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702 * coverage1 and coverage2 : These two columns show the coverage near breakpoint1 and breakpoint2, respectively. The coverage is calculated as the number of fragments near the breakpoint on the side of the breakpoint that is retained in the fusion transcript. Note that the coverage calculation counts all fragments (even duplicates), whereas the columns split_reads1, split_reads2, and discordant_mates only count non-discarded reads. Fragments discarded due to being duplicates or other types of artifacts can be found in the column filters.
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703
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704 * confidence : Each prediction is assigned one of the confidences low, medium, or high. Several characteristics are taken into account, including: the number of supporting reads, the balance of split reads and discordant mates, the distance between the breakpoints, the type of event, whether the breakpoints are intragenic or not, and whether there are other events which corroborate the prediction, e.g. multiple isoforms or balanced translocations. See section Interpretation of results for further advice on judging the credibility of predictions.
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705
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706 * reading_frame : This column states whether the gene at the 3' end of the fusion is fused in-frame or out-of-frame. The value stop-codon indicates that there is a stop codon prior to the fusion junction, such that the 3' end is not translated, even if the reading frame is preserved across the junction. The prediction of the reading frame builds on the prediction of the peptide sequence. A dot (.) indicates that the peptide sequence cannot be predicted, for example, because the transcript sequence could not be determined or because the breakpoint of the 5' gene does not overlap a coding region.
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707
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708 * tags : When a user-defined list of tags is provided via the parameter -t, this column is populated with the provided tag whenever a fusion matches the coordinates specified for the respective tag. When multiple tags match, they are separated by a comma.
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709
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710 * retained_protein_domains : If Arriba is provided with protein domain annotation using the parameter -p, then this column is populated with protein domains retained in the fusion. Multiple protein domains are separated by a comma. Redundant protein domains are only listed once. After every domain the fraction that is retained is stated as a percentage value in parentheses. The protein domains of the 5' and 3' genes are separated by a pipe symbol (|).
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711
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712 * closest_genomic_breakpoint1 and closest_genomic_breakpoint2 : When a matched whole-genome sequencing sample is available, one can feed structural variant calls obtained therefrom into Arriba (see parameter -d). Arriba then considers this information during fusion calling, which improves the overall accuracy. These two columns contain the coordinates of the genomic breakpoints which are closest to the transcriptomic breakpoints given in the columns breakpoint1 and breakpoint2. The values in parentheses are the distances between transcriptomic and genomic breakpoints.
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713
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714 * gene_id1 and gene_id2 : These two columns state the identifiers of the fused genes as given in the gene_id attribute in the GTF file.
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715
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716 * transcript_id1 and transcript_id2 : For both fused genes, Arriba determines the best matching isoform that is transcribed as part of the fusion. The isoform is selected by how well its annotated exons match the splice pattern of the supporting reads of a fusion.
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717
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718 * direction1 and direction2 : These columns indicate the orientation of the fusion. A value of downstream means that the partner is fused downstream of the breakpoint, i.e. at a coordinate higher than the breakpoint. A value of upstream means the partner is fused at a coordinate lower than the breakpoint. When the prediction of the strands or of the 5' gene fails, this information gives insight into which parts of the fused genes are retained in the fusion.
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719
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720 * filters : This column lists the filters which removed one or more of the supporting reads. The section Internal algorithm describes all filters in detail. The number of filtered reads is given in parentheses after the name of the filter. The total number of supporting reads can be obtained by summing up the reads given in the columns split_reads1, split_reads2, discordant_mates, and filters. If a filter discarded the event as a whole (all reads), the number of filtered reads is not stated.
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721
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722 * fusion_transcript : This column contains the fusion transcript sequence. The sequence is assembled from the supporting reads of the most highly expressed transcript. It represents the transcript isoform that is most likely expressed according to the splice patterns of the supporting reads. The column contains a dot (.), when the sequence could not be predicted. This is the case when the strands or the 5' end of the transcript could not be predicted reliably. The breakpoint is represented as a pipe symbol (|). When non-template bases are inserted between the fused genes, these bases are represented as lowercase letters between two pipes. Reference mismatches (SNPs or SNVs) are indicated as lowercase letters, insertions as bases between brackets ([ and ]), deleted bases as one or more dashes (-), introns as three underscores (___), and ambiguous positions, such as positions with diverse reference mismatches, are represented as ?. Missing information due to insufficient coverage is denoted as an ellipsis (...). If the switch -I is used, then an attempt is made to fill missing information with the assembly sequence. A sequence stretch that was taken from the assembly sequence rather than the supporting reads is wrapped in parentheses (( and )). In addition, when -I is used, the sequence is trimmed to the boundaries of the fused transcripts. The coordinate of the fusion breakpoint relative to the start of the transcript can thus easily be inferred by counting the bases from the beginning of the fusion transcript to the breakpoint character (|). In case the full sequence could be constructed from the combined information of supporting reads and assembly sequence, the start of the fusion transcript is marked by a caret sign (^) and the end by a dollar sign ($). If the full sequence could not be constructed, these signs are missing.
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723
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724 * peptide_sequence : This column contains the fusion peptide sequence. The sequence is translated from the fusion transcript given in the column fusion_transcript and determines the reading frame of the fused genes according to the transcript isoforms given in the columns transcript_id1 and transcript_id2. Translation starts at the start of the assembled fusion transcript or when the start codon is encountered in the 5' gene. Translation ends when either the end of the assembled fusion transcript is reached or when a stop codon is encountered. If the fusion transcript contains an ellipsis (...), the sequence beyond the ellipsis is trimmed before translation, because the reading frame cannot be determined reliably. The column contains a dot (.), when the transcript sequence could not be predicted or when the precise breakpoints are unknown due to lack of split reads or when the fusion transcript does not overlap any coding exons in the 5' gene or when no start codon could be found in the 5' gene or when there is a stop codon prior to the fusion junction (in which case the column reading_frame contains the value stop-codon). The breakpoint is represented as a pipe symbol (|). If a codon spans the breakpoint, the amino acid is placed on the side of the breakpoint where two of the three bases reside. Codons resulting from non-template bases are flanked by two pipes. Amino acids are written as lowercase characters in the following situations: non-silent SNVs/SNPs, insertions, frameshifts, codons spanning the breakpoint, non-coding regions (introns/intergenic regions/UTRs), and non-template bases. Codons which cannot be translated to amino acids, such as those having invalid characters, are represented as ?.
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725
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726 * read_identifiers : This column contains the names of the supporting reads separated by commas.
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727
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728 - fusions.discarded.tsv
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729
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730 The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv.
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731
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732
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733 **VISUALIZATION**
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734
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735 See: https://arriba.readthedocs.io/en/latest/visualization/
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736
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737 - fusions.pdf
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738
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739 A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint.
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740
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741 .. image:: draw-fusions-example.png
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742 :width: 800
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743 :height: 467
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744
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745
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746 .. _Arriba: https://arriba.readthedocs.io/en/latest/
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747 .. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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748 .. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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749 .. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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750 .. _OPTIONS: https://arriba.readthedocs.io/en/latest/command-line-options/
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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751
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
iuc
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752 ]]></help>
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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753 <expand macro="citations" />
a24ca22b906e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit b12158e6cc9b1b2bd6e7522dfc183e9055575823
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754 </tool>