Mercurial > repos > iuc > arriba_draw_fusions

comparison macros.xml @ 5:cf01dd6c6b1f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 3a528b3f87cff585baf4abb8ebe0be95a24044ea
author iuc
date Wed, 25 Oct 2023 08:24:28 +0000
parents 31f8063eedea
children
comparison
equal deleted inserted replaced
4:31f8063eedea 5:cf01dd6c6b1f
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.4.0</token> 2 <token name="@TOOL_VERSION@">2.4.0</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>
51 #if $genome.assembly 51 #if $genome.assembly
52 #set $genome_assembly = 'genome.fa' 52 #set $genome_assembly = 'genome.fa'
53 ln -sf '$genome.assembly' $genome_assembly && 53 ln -sf '$genome.assembly' $genome_assembly &&
54 #end if 54 #end if
55 #elif str($genome.genome_source) == "cached" 55 #elif str($genome.genome_source) == "cached"
56 #set $genome_assembly = $genome.ref_file.fields.fasta 56 #set $genome_assembly = $genome.ref_file.fields.path
57 #end if 57 #end if
58 ]]></token> 58 ]]></token>
59 <token name="@GTF_SOURCE@"><![CDATA[ 59 <token name="@GTF_SOURCE@"><![CDATA[
60 #if str($genome_gtf.gtf_source) == "history" 60 #if str($genome_gtf.gtf_source) == "history"
61 ln -sf '$genome_gtf.annotation' genome.gtf && 61 ln -sf '$genome_gtf.annotation' genome.gtf &&
62 #end if 62 #end if
63 ]]></token> 63 ]]></token>
64 64
65 <xml name="visualization_options"> 65 <xml name="visualization_options">
66 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> 66 <param argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
67 <section name="options" expanded="false" title="Draw Fusion Options"> 67 <section name="options" expanded="false" title="Draw Fusion Options">
68 <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/> 68 <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>
69 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection"> 69 <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
70 <help>By default the transcript isoform with the highest coverage is drawn. 70 <help>By default the transcript isoform with the highest coverage is drawn.
71 Alternatively, the transcript isoform that is provided in the columns 71 Alternatively, the transcript isoform that is provided in the columns