Mercurial > repos > iuc > bcftools_convert_to_vcf

comparison bcftools_convert_to_vcf.xml @ 25:48d346686fc3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:59:20 +0000
parents feb68597f5bc
children
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24:a40ff7d1a8d3 25:48d346686fc3
9 <expand macro="requirements"> 9 <expand macro="requirements">
10 <expand macro="samtools_requirement"/> 10 <expand macro="samtools_requirement"/>
11 </expand> 11 </expand>
12 <expand macro="version_command" /> 12 <expand macro="version_command" />
13 <command detect_errors="aggressive"><![CDATA[ 13 <command detect_errors="aggressive"><![CDATA[
14 @PREPARE_ENV@
15 #set $input_vcf = None 14 #set $input_vcf = None
16 #if $convert.convert_from == 'gvcf': 15 #if $convert.convert_from == 'gvcf':
17 #set $input_vcf = 'input.vcf.gz' 16 #set $input_vcf = 'input.vcf.gz'
18 #if $convert.input_file.is_of_type('vcf') 17 #if $convert.input_file.is_of_type('vcf')
19 bgzip -c '$convert.input_file' > $input_vcf && 18 bgzip -c '$convert.input_file' > $input_vcf &&
209 208
210 Converts other variant formats to vcf. See man page for file formats details. 209 Converts other variant formats to vcf. See man page for file formats details.
211 210
212 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 211 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
213 212
214 @BCFTOOLS_WIKI@ 213 @BCFTOOLS_HOWTOS@
215 ]]> 214 ]]>
216 </help> 215 </help>
217 <expand macro="citations" /> 216 <expand macro="citations" />
218 </tool> 217 </tool>