Mercurial > repos > iuc > arriba_get_filters

comparison macros.xml @ 1:1fe9d667447c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 5def6a1b52ea9116547b5fd953a45b9ef85a011f
author iuc
date Fri, 23 Sep 2022 13:49:51 +0000
parents 125d20cb23d7
children 47311adce34e
comparison
equal deleted inserted replaced
0:125d20cb23d7 1:1fe9d667447c
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.3.0</token> 2 <token name="@TOOL_VERSION@">2.3.0</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>
56 #set $genome_assembly = $genome.ref_file.fields.fasta 56 #set $genome_assembly = $genome.ref_file.fields.fasta
57 #end if 57 #end if
58 ]]></token> 58 ]]></token>
59 <token name="@GTF_SOURCE@"><![CDATA[ 59 <token name="@GTF_SOURCE@"><![CDATA[
60 #if str($genome_gtf.gtf_source) == "history" 60 #if str($genome_gtf.gtf_source) == "history"
61 #if $genome_gtf.annotation.is_of_type('gtf.gz') 61 ln -sf '$genome_gtf.annotation' genome.gtf &&
62 #set $genome_annotation = 'genome.gtf.gz'
63 #else
64 #set $genome_annotation = 'genome.gtf'
65 #end if
66 ln -sf '$genome_gtf.annotation' $genome_annotation &&
67 #end if 62 #end if
68 ]]></token> 63 ]]></token>
69 64
70 <xml name="visualization_options"> 65 <xml name="visualization_options">
71 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> 66 <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
298 --pdfWidth=$visualization.options.pdfWidth 293 --pdfWidth=$visualization.options.pdfWidth
299 #end if 294 #end if
300 #if str($visualization.options.pdfHeight) 295 #if str($visualization.options.pdfHeight)
301 --pdfHeight=$visualization.options.pdfHeight 296 --pdfHeight=$visualization.options.pdfHeight
302 #end if 297 #end if
303 # fontFamily
304 #if $visualization.options.fontFamily 298 #if $visualization.options.fontFamily
305 --fontFamily=$visualization.options.fontFamily 299 --fontFamily=$visualization.options.fontFamily
306 #end if 300 #end if
307 #if str($visualization.options.fontSize) 301 #if str($visualization.options.fontSize)
308 --fontSize=$visualization.options.fontSize 302 --fontSize=$visualization.options.fontSize