Mercurial > repos > iuc > hal_maf2hal
changeset 1:560852609a4c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools commit 30ac0af6dfa729277011bcd73cd5560efa03fb97
| author | iuc |
|---|---|
| date | Wed, 18 Mar 2026 15:07:59 +0000 |
| parents | 2900728b299a |
| children | |
| files | hal_maf2hal.xml macros.xml test-data/halAddToBranch_bot_input.hal test-data/halAddToBranch_top_input.hal test-data/halTestExtended.hal |
| diffstat | 5 files changed, 6 insertions(+), 5 deletions(-) [+] |
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--- a/hal_maf2hal.xml Fri Feb 06 10:37:03 2026 +0000 +++ b/hal_maf2hal.xml Wed Mar 18 15:07:59 2026 +0000 @@ -12,12 +12,12 @@ cp '$mode.input_hal' writable_hal.hal && #end if ## Uncompress input - #if $input_maf.ext.endswith('.gz'): + #if $input_maf.is_of_type('maf.gz'): gunzip -c '$input_maf' > uncompressed_input.maf && - #else if $input_maf.ext.endswith('.bz2'): + #else if $input_maf.is_of_type('maf.bz2'): bunzip2 -c '$input_maf' > uncompressed_input.maf && #else - cp '$input_maf' uncompressed_input.maf && + ln -s '$input_maf' uncompressed_input.maf && #end if maf2hal #if $refGenome:
--- a/macros.xml Fri Feb 06 10:37:03 2026 +0000 +++ b/macros.xml Wed Mar 18 15:07:59 2026 +0000 @@ -4,8 +4,9 @@ <requirement type="package" version="@TOOL_VERSION@">cactus</requirement> </requirements> </xml> - <token name="@TOOL_VERSION@">2.9.9</token> + <token name="@TOOL_VERSION@">3.1.4</token> <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX_HAL2VG@">1</token> <token name="@PROFILE@">25.1</token> <xml name="stdio"> <stdio> @@ -171,7 +172,7 @@ <validator type="regex" message="Enter without leading or trailing spaces">^\S(?:.*\S)?$</validator> </xml> <xml name="validator_comma_list"> - <validator type="regex" message="Enter a comma separated list of genomes, without leading or trailing spaces">^\S(?:[^,]*\S)?(?:,\S(?:[^,]*\S)?)*$</validator> + <validator type="regex" message="Enter a comma separated list of genomes, without leading or trailing spaces">^[^,\s]+(,[^,\s]+)*$</validator> </xml> <xml name="validator_newick"> <validator type="regex" message="Enter a Newick tree">^.*;$</validator>