annotate macros.xml @ 1:55ca46d68a57 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
author jjohnson
date Mon, 13 Jun 2022 12:10:34 +0000
parents 7345cb1bb772
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
1 <macros>
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
2 <token name="@TOOL_VERSION@">2.3.0</token>
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
3 <token name="@VERSION_SUFFIX@">0</token>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
4 <xml name="requirements">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
5 <requirements>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
7 <yield/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
8 </requirements>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
9 </xml>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
10 <xml name="citations">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
11 <citations>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
12 <citation type="doi">10.1101/gr.257246.119</citation>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
13 <yield />
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
14 </citations>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
15 </xml>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
16 <xml name="version_command">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
17 <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
18 </xml>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
19 <xml name="genome_source" token_assembly_optional="false" >
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
20 <conditional name="genome">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
21 <param name="genome_source" type="select" label="Arriba Genome assembly and annotation source">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
22 <option value="history">From your history</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
23 <option value="cached">Use built-in Arriba</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
24 </param>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
25 <when value="history">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
26 <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
27 <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
28 </when>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
29 <when value="cached">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
30 <param name="arriba_ref" type="select" label="Arriba Genome assembly and annotation">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
31 <options from_data_table="arriba_indexes">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
32 </options>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
33 </param>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
34 </when>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
35 </conditional>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
36 </xml>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
37 <token name="@GENOME_SOURCE@">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
38 #if str($genome.genome_source) == "history"
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
39 #if $genome.assembly
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
40 #set $genome_assembly = $genome.assembly
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
41 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
42 #set $genome_annotation = $genome.annotation
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
43 #else
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
44 #set $genome_assembly = $genome.arriba_ref.fields.fasta
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
45 #set $genome_annotation = $genome.arriba_ref.fields.gtf
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
46 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
47 </token>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
48
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
49 <xml name="visualization_options">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
50 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
51 <section name="options" expanded="false" title="Draw Fusion Options">
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
52 <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
53 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
54 <help>By default the transcript isoform with the highest coverage is drawn.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
55 Alternatively, the transcript isoform that is provided in the columns
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
56 transcript_id1 and transcript_id2 in the given fusions file can be drawn.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
57 Selecting the isoform with the highest coverage usually produces nicer plots,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
58 in the sense that the coverage track is smooth and shows a visible increase in coverage after the fusion breakpoint.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
59 However, the isoform with the highest coverage may not be the one that is involved in the fusion.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
60 Often, genomic rearrangements lead to non-canonical isoforms being transcribed.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
61 For this reason, it can make sense to rely on the transcript selection provided by the columns transcript_id1/2,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
62 which reflect the actual isoforms involved in a fusion.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
63 \ As a third option, the transcripts that are annotated as canonical can be drawn.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
64 Transcript isoforms tagged with appris_principal, appris_candidate, or CCDS are considered canonical.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
65 </help>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
66 <option value="coverage">coverage</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
67 <option value="provided">provided</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
68 <option value="canonical">canonical</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
69 </param>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
70 <param argument="--minConfidenceForCircosPlot" type="select" optional="true" label="Transcript selection">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
71 <help>The fusion of interest is drawn as a solid line in the circos plot.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
72 To give an impression of the overall degree of rearrangement,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
73 all other fusions are drawn as semi-transparent lines in the background.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
74 This option determines which other fusions should be included in the circos plot.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
75 Values specify the minimum confidence a fusion must have to be included.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
76 It usually makes no sense to include low-confidence fusions in circos plots,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
77 because they are abundant and unreliable, and would clutter up the circos plot.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
78 Default: medium
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
79 </help>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
80 <option value="none">none - only the fusion of interest is drawn</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
81 <option value="low">low</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
82 <option value="medium">medium</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
83 <option value="high">high</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
84 </param>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
85 <param argument="--squishIntrons" type="select" optional="true" label="Squish introns">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
86 <help>Exons usually make up only a small fraction of a gene.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
87 They may be hard to see in the plot. i
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
88 Since introns are in most situations of no interest in the context of gene fusions,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
89 this switch can be used to shrink the size of introns to a fixed, negligible size.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
90 It makes sense to disable this feature, if breakpoints in introns are of importance.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
91 Default: TRUE
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
92 </help>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
93 <option value="TRUE">True</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
94 <option value="FALSE">False</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
95 </param>
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
96 <param argument="--showIntergenicVicinity" type="text" value="" optional="true" label="Intergenic Vicinity">
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
97 <help>This option only applies to intergenic breakpoints.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
98 If it is set to a value greater than 0, then the script draws the genes
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
99 which are no more than the given distance away from an intergenic breakpoint.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
100 The keywords closestGene and closestProteinCodingGene instruct the script
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
101 to dynamically determine the distance to the next (protein-coding) gene for each breakpoint.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
102 Alternatively, instead of specifying a single distance
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
103 that is applied upstream and downstream of both breakpoints alike,
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
104 more fine-grained control over the region to be shown is possible by specifying four comma-separated values.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
105 The first two values determine the region to the left and to the right of breakpoint 1;
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
106 the third and fourth values determine the region to the left and to the right of breakpoint 2.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
107 Note that this option is incompatible with squishIntrons.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
108 Default: 0
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
109 </help>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
110 <option value="closestGene">closestGene</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
111 <option value="closestProteinCodingGene">closestProteinCodingGene</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
112 <validator type="regex" message="">^(closestGene|closestProteinCodingGene|\d+|\d+,\d+,\d+,\d+)$</validator>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
113 </param>
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
114 <param argument="--mergeDomainsOverlappingBy" type="float" value="" min="0." max="1.0" optional="true" label="Merge Domains Overlapping By">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
115 <help>Occasionally, domains are annotated redundantly.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
116 For example, tyrosine kinase domains are frequently annotated as
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
117 Protein tyrosine kinase and Protein kinase domain.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
118 In order to simplify the visualization, such domains can be merged into one,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
119 given that they overlap by the given fraction.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
120 The description of the larger domain is used.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
121 Default: 0.9
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
122 </help>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
123 </param>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
124 <param argument="--printExonLabels" type="select" optional="true" label="Print Exon Labels">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
125 <help>By default the number of an exon is printed inside each exon,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
126 which is taken from the attribute exon_number of the GTF annotation.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
127 When a gene has many exons, the boxes may be too narrow to contain the labels,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
128 resulting in unreadable exon labels. In these situations, i
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
129 it may be better to turn off exon labels.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
130 Default: TRUE
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
131 </help>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
132 <option value="TRUE">True</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
133 <option value="FALSE">False</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
134 </param>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
135 <param argument="--render3dEffect" type="select" optional="true" label="Render 3D effect">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
136 <help>Whether light and shadow should be rendered to give objects a 3D effect.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
137 Default: TRUE
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
138 </help>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
139 <option value="TRUE">True</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
140 <option value="FALSE">False</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
141 </param>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
142 <param argument="--optimizeDomainColors" type="select" optional="true" label="Optimize Domain Colors">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
143 <help>By default, the script colorizes domains according to the colors
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
144 specified in the file given in --annotation.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
145 This way, coloring of domains is consistent across all proteins.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
146 But since there are more distinct domains than colors,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
147 this can lead to different domains having the same color.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
148 If this option is set to TRUE, the colors are recomputed for each fusion separately.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
149 This ensures that the colors have the maximum distance for each individual fusion,
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
150 but they are no longer consistent across different fusions.
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
151 Default: FALSE
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
152 </help>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
153 <option value="TRUE">True</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
154 <option value="FALSE">False</option>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
155 </param>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
156 <param argument="--color1" type="color" value="" optional="true" label="Color of the 5' end of the fusion."/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
157 <param argument="--color2" type="color" value="" optional="true" label="Color of the 3' end of the fusion."/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
158 <param argument="--pdfWidth" type="float" value="" min="1." optional="true" label="Width of PDF output file in inches"
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
159 help="Default: 11.692"/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
160 <param argument="--pdfHeight" type="float" value="" min="1." optional="true" label="Height of PDF output file in inches"
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
161 help="Default: 8.267"/>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
162 <param argument="--fontSize" type="float" value="" min="0." optional="true" label="Scale the size of text"
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
163 help="Default: 1.0"/>
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
164 <param argument="--fontFamily" type="text" value="" optional="true" label="Font to use for all labels in the plots.">
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
165 <help>Default: Helvetica
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
166 </help>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
167 <option value="serif">serif</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
168 <option value="sans">sans</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
169 <option value="mono">mono</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
170 <option value="AvantGarde">AvantGarde</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
171 <option value="Bookman">Bookman</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
172 <option value="Courier">Courier</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
173 <option value="Helvetica">Helvetica</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
174 <option value="Helvetica-Narrow">Helvetica-Narrow</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
175 <option value="NewCenturySchoolbook">NewCenturySchoolbook</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
176 <option value="Palatino">Palatino</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
177 <option value="Times">Times</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
178 <option value="URWGothic">URWGothic</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
179 <option value="URWBookman">URWBookman</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
180 <option value="NimbusMon">NimbusMon</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
181 <option value="NimbusSan">NimbusSan</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
182 <option value="URWHelvetica">URWHelvetica</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
183 <option value="NimbusSanCond">NimbusSanCond</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
184 <option value="CenturySch">CenturySch</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
185 <option value="URWPalladio">URWPalladio</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
186 <option value="NimbusRom">NimbusRom</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
187 <option value="URWTimes">URWTimes</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
188 <option value="ArialMT">ArialMT</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
189 <option value="Japan1">Japan1</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
190 <option value="Japan1HeiMin">Japan1HeiMin</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
191 <option value="Japan1GothicBBB">Japan1GothicBBB</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
192 <option value="Japan1Ryumin">Japan1Ryumin</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
193 <option value="Korea1">Korea1</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
194 <option value="Korea1deb">Korea1deb</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
195 <option value="CNS1">CNS1</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
196 <option value="GB1">GB1</option>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
197 </param>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
198 <param argument="--fixedScale" type="integer" value="" min="0" optional="true" label="Apply a fixed scale to all fusions">
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
199 <help>By default, transcripts are scaled automatically to fill the entire page.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
200 This parameter enforces a fixed scale to be applied to all fusions,
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
201 which is useful when a collection of fusions should be visualized and the sizes of all transcripts should be comparable.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
202 A common use case is the visualization of a gene that is found to be fused to multiple partners.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
203 By forcing all fusion plots to use the same scale, the fusions can be summarized as a collage
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
204 in a single plot one above the other with matching scales.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
205 Note: The scale must be bigger than the sum of the biggest pair of transcripts to be drawn,
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
206 or else dynamic scaling is applied, because display errors would occur otherwise.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
207 The default value is 0, which means that no fixed scale should be used
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
208 and that the scale should be adapted dynamically for each fusion. Default: 0
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
209 </help>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
210 </param>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
211 <param argument="--coverageRange" type="text" value="" optional="true" label="Maximum coverage for plot">
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
212 <help>When the parameter --alignments is used, coverage plots are drawn above the transcripts of the fused genes.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
213 The plots can be cropped at a fixed level by passing a non-zero value to this parameter.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
214 When only a single value is given, both coverage plots (for gene1 and gene2) are cropped at the same level.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
215 When two comma-separated values are given, the cutoffs can be specified independently for the two plots.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
216 A value of 0 indicates that no cropping should be applied (i.e., the cutoff is set to the peak coverage)
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
217 and that the coverage plots of both genes should be on the same scale. This is the default behavior.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
218 A value of 0,0 also indicates that no cropping should be applied,
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
219 but the coverage plots of the two genes have different scales:
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
220 each one is scaled individually to the peak coverage of the respective gene.
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
221 Default: 0
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
222 </help>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
223 <validator type="regex" message="">^\d+(,\d+)?$</validator>
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
224 </param>
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
225 </section>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
226 </xml>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
227 <token name="@DRAW_FUSIONS@">
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
228 draw_fusions.R
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
229 --fusions='$fusions'
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
230 --alignments='Aligned.sortedByCoord.out.bam'
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
231 --annotation='$genome.annotation'
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
232 --output=fusions.pdf
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
233 #if $visualization.cytobands
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
234 --cytobands='$visualization.cytobands'
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
235 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
236 #if $protein_domains
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
237 --proteinDomains='$protein_domains'
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
238 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
239 ## Visualization Options
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
240 #if $visualization.options.transcriptSelection
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
241 --transcriptSelection=$visualization.options.transcriptSelection
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
242 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
243 #if $visualization.options.minConfidenceForCircosPlot
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
244 --minConfidenceForCircosPlot=$visualization.options.minConfidenceForCircosPlot
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
245 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
246 #if $visualization.options.squishIntrons
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
247 --squishIntrons=$visualization.options.squishIntrons
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
248 #if $visualization.options.squishIntrons == 'FALSE' and $visualization.options.showIntergenicVicinity
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
249 --showIntergenicVicinity=$visualization.options.showIntergenicVicinity
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
250 #end if
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
251 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
252 #if $visualization.options.mergeDomainsOverlappingBy
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
253 --mergeDomainsOverlappingBy=$visualization.options.mergeDomainsOverlappingBy
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
254 #end if
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
255 #if $visualization.options.sampleName
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
256 --sampleName=$visualization.options.sampleName
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
257 #end if
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
258 #if $visualization.options.printExonLabels
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
259 --printExonLabels=$visualization.options.printExonLabels
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
260 #end if
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
261 #if $visualization.options.coverageRange
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
262 --coverageRange="$visualization.options.coverageRange"
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
263 #end if
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
264 #if $visualization.options.render3dEffect
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
265 --render3dEffect=$visualization.options.render3dEffect
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
266 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
267 #if $visualization.options.optimizeDomainColors
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
268 --optimizeDomainColors=$visualization.options.optimizeDomainColors
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
269 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
270 #if $visualization.options.color1
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
271 --color1=$visualization.options.color1
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
272 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
273 #if $visualization.options.color2
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
274 --color2=$visualization.options.color2
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
275 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
276 #if $visualization.options.pdfWidth
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
277 --pdfWidth=$visualization.options.pdfWidth
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
278 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
279 #if $visualization.options.pdfHeight
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
280 --pdfHeight=$visualization.options.pdfHeight
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
281 #end if
1
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
282 # fontFamily
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
283 #if $visualization.options.fontFamily
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
284 --fontFamily=$visualization.options.fontFamily
55ca46d68a57 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 25fe476002a414e72f33868ba356a3ca4f86865d"
jjohnson
parents: 0
diff changeset
285 #end if
0
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
286 #if $visualization.options.fontSize
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
287 --fontSize=$visualization.options.fontSize
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
288 #end if
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
289 </token>
7345cb1bb772 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit c1d05da7c2c76feae94cbc640be7b010f31397d2-dirty"
jjohnson
parents:
diff changeset
290 </macros>