Mercurial > repos > iuc > hal_halcoverage
changeset 1:36cea1c55698 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 15:07:12 +0000 |
| parents | 48d453b8f39d |
| children | |
| files | hal_halCoverage.xml macros.xml test-data/halAddToBranch_bot_input.hal test-data/halAddToBranch_top_input.hal test-data/halTestExtended.hal |
| diffstat | 5 files changed, 10 insertions(+), 9 deletions(-) [+] |
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--- a/hal_halCoverage.xml Fri Feb 06 10:39:17 2026 +0000 +++ b/hal_halCoverage.xml Wed Mar 18 15:07:12 2026 +0000 @@ -12,7 +12,7 @@ --seed $seed $bySequence ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree. - '$input_hal' '$refGenome' | tr ',' '\t' > '$out_file' + '$input_hal' '$refGenome' | sed $'s/, */\t/g' > '$out_file' ]]></command> <inputs> <expand macro="input_hal"/> @@ -31,8 +31,8 @@ <param name="seed" value="100"/> <output name="out_file" ftype="tabular"> <assert_contents> - <has_line line="Genome	 sitesCovered1Times	 sitesCovered2Times	 sitesCovered3Times	 sitesCovered4Times	 sitesCovered5Times"/> - <has_line line="Genome_2	 856475	 482343	 482343	 214021	 0"/> + <has_line line="Genome	sitesCovered1Times	sitesCovered2Times	sitesCovered3Times	sitesCovered4Times	sitesCovered5Times"/> + <has_line line="Genome_2	856475	482343	482343	214021	0"/> <has_n_lines n="4"/> </assert_contents> </output> @@ -44,8 +44,8 @@ <param name="seed" value="100"/> <output name="out_file" ftype="tabular"> <assert_contents> - <has_line line="Genome	 sitesCovered1Times	 sitesCovered2Times	 sitesCovered3Times	 sitesCovered4Times	 sitesCovered5Times"/> - <has_line line="Genome_2	 839	 500	 500	 233	 0"/> + <has_line line="Genome	sitesCovered1Times	sitesCovered2Times	sitesCovered3Times	sitesCovered4Times	sitesCovered5Times"/> + <has_line line="Genome_2	839	500	500	233	0"/> <has_n_lines n="4"/> </assert_contents> </output> @@ -57,8 +57,8 @@ <param name="seed" value="100"/> <output name="out_file" ftype="tabular"> <assert_contents> - <has_line line="Genome	 sitesCovered1Times	 sitesCovered2Times	 sitesCovered3Times	 sitesCovered4Times	 sitesCovered5Times"/> - <has_line line="Genome_2	 856475	 482343	 482343	 214021	 0"/> + <has_line line="Genome	sitesCovered1Times	sitesCovered2Times	sitesCovered3Times	sitesCovered4Times	sitesCovered5Times"/> + <has_line line="Genome_2	856475	482343	482343	214021	0"/> <has_line line="Coverage on Genome_1_seq"/> <has_n_lines n="9"/> </assert_contents>
--- a/macros.xml Fri Feb 06 10:39:17 2026 +0000 +++ b/macros.xml Wed Mar 18 15:07:12 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>