Mercurial > repos > iuc > arriba_draw_fusions

comparison macros.xml @ 4:ea76fa4f1526 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 26aa67fb926f54dfda456f8e25b3c3a21aa63685
author iuc
date Wed, 25 Sep 2024 15:29:42 +0000
parents ca7d9d9f44d6
children c49d6a069ce3
comparison
equal deleted inserted replaced
3:ca7d9d9f44d6 4:ea76fa4f1526
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@">2</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