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comparison macros.xml @ 9:8c4c97fd0555 draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bd2c6bea7cb7dc30ca57f9d69ad49460ddf7f14b"
author jjohnson
date Wed, 13 Oct 2021 18:45:16 +0000
parents 25d207f7ff83
children c58d1774c762
comparison
equal deleted inserted replaced
8:1a56888ddb7d 9:8c4c97fd0555
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.1.0</token> 2 <token name="@TOOL_VERSION@">2.1.0</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
7 <yield/> 7 <yield/>
8 </requirements> 8 </requirements>
14 </citations> 14 </citations>
15 </xml> 15 </xml>
16 <xml name="version_command"> 16 <xml name="version_command">
17 <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command> 17 <version_command>arriba -h | grep Version | sed 's/^.* //'</version_command>
18 </xml> 18 </xml>
19 <xml name="genome_source" token_assembly_optional="false" >
20 <conditional name="genome">
21 <param name="genome_source" type="select" label="Arriba Genome assembly and annotation source">
22 <option value="history">From your history</option>
23 <option value="cached">Use built-in Arriba</option>
24 </param>
25 <when value="history">
26 <param name="assembly" argument="-a" type="data" format="fasta" optional="@ASSEMBLY_OPTIONAL@" label="Genome assembly fasta"/>
27 <param name="annotation" argument="-g" type="data" format="gtf" label="Gene annotation in GTF format"/>
28 </when>
29 <when value="cached">
30 <param name="arriba_ref" type="select" label="Arriba Genome assembly and annotation">
31 <options from_data_table="arriba_indexes">
32 </options>
33 </param>
34 </when>
35 </conditional>
36 </xml>
37 <token name="@GENOME_SOURCE@">
38 #if str($genome.genome_source) == "history"
39 #if $genome.assembly
40 #set $genome_assembly = $genome.assembly
41 #end if
42 #set $genome_annotation = $genome.annotation
43 #else
44 #set $genome_assembly = $genome.arriba_ref.fields.fasta
45 #set $genome_annotation = $genome.arriba_ref.fields.gtf
46 #end if
47 </token>
48
19 <xml name="visualization_options"> 49 <xml name="visualization_options">
20 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> 50 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
21 <section name="options" expanded="false" title="Draw Fusion Options"> 51 <section name="options" expanded="false" title="Draw Fusion Options">
22 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection"> 52 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
23 <help>By default the transcript isoform with the highest coverage is drawn. 53 <help>By default the transcript isoform with the highest coverage is drawn.
125 </xml> 155 </xml>
126 <token name="@DRAW_FUSIONS@"> 156 <token name="@DRAW_FUSIONS@">
127 draw_fusions.R 157 draw_fusions.R
128 --fusions='$fusions' 158 --fusions='$fusions'
129 --alignments='Aligned.sortedByCoord.out.bam' 159 --alignments='Aligned.sortedByCoord.out.bam'
130 --annotation='$annotation' 160 --annotation='$genome.annotation'
131 --output=fusions.pdf 161 --output=fusions.pdf
132 #if $visualization.cytobands 162 #if $visualization.cytobands
133 --cytobands='$visualization.cytobands' 163 --cytobands='$visualization.cytobands'
134 #end if 164 #end if
135 #if $protein_domains 165 #if $protein_domains