Mercurial > repos > iuc > hal_maf2hal

comparison hal_maf2hal.xml @ 1:8af265f90d58 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit f46096b336bf460424143fc9d633b5e7c20bf1cf
author iuc
date Thu, 05 Mar 2026 11:32:14 +0000
parents 0cfe56c4ac68
children
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0:0cfe56c4ac68 1:8af265f90d58
10 #if $mode.append == 'true': 10 #if $mode.append == 'true':
11 ## If an input HAL file is provided to append to, ensure that it is not modified. 11 ## If an input HAL file is provided to append to, ensure that it is not modified.
12 cp '$mode.input_hal' writable_hal.hal && 12 cp '$mode.input_hal' writable_hal.hal &&
13 #end if 13 #end if
14 ## Uncompress input 14 ## Uncompress input
15 #if $input_maf.ext.endswith('.gz'): 15 #if $input_maf.is_of_type('maf.gz'):
16 gunzip -c '$input_maf' > uncompressed_input.maf && 16 gunzip -c '$input_maf' > uncompressed_input.maf &&
17 #else if $input_maf.ext.endswith('.bz2'): 17 #else if $input_maf.is_of_type('maf.bz2'):
18 bunzip2 -c '$input_maf' > uncompressed_input.maf && 18 bunzip2 -c '$input_maf' > uncompressed_input.maf &&
19 #else 19 #else
20 cp '$input_maf' uncompressed_input.maf && 20 ln -s '$input_maf' uncompressed_input.maf &&
21 #end if 21 #end if
22 maf2hal 22 maf2hal
23 #if $refGenome: 23 #if $refGenome:
24 --refGenome '$refGenome' 24 --refGenome '$refGenome'
25 #end if 25 #end if