Mercurial > repos > iuc > hal_halsnps
changeset 2:9c83aa0e3e6a 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 15:21:28 +0000 |
| parents | 50336dc82da7 |
| children | |
| files | hal_halSnps.xml macros.xml test-data/halAddToBranch_bot_input.hal test-data/halAddToBranch_top_input.hal test-data/halTestExtended.hal |
| diffstat | 5 files changed, 31 insertions(+), 2 deletions(-) [+] |
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--- a/hal_halSnps.xml Thu Mar 05 11:35:43 2026 +0000 +++ b/hal_halSnps.xml Wed Mar 18 15:21:28 2026 +0000 @@ -16,6 +16,9 @@ --start $start --length $length --minSpeciesForSnp $minSpeciesForSnp + #if $tsv: + --tsv '$out_file_detail' + #end if $noDupes $unique '$input_hal' '$refGenome' '$targetGenomes' @@ -39,11 +42,15 @@ <expand macro="params_start"/> <expand macro="params_length"/> <param argument="--noDupes" type="boolean" truevalue="--noDupes" falsevalue="" checked="false" label="No duplicates" help="Do not consider paralogies while mapping"/> + <param argument="--tsv" type="boolean" truevalue="--tsv" falsevalue="" checked="false" label="Detailed SNPs file" help="Create a detailed file containing base assignments for each genome at SNP locations"/> <param argument="--minSpeciesForSnp" type="integer" min="1" value="1" label="Minimum number of species" help="Minimum number of species that must have a different base than the reference for a SNP to be reported in the output"/> <param argument="--unique" type="boolean" truevalue="--unique" falsevalue="" checked="false" label="Unique" help="Whether to ignore columns that are not canonical on the reference genome"/> </inputs> <outputs> <data name="out_file" format="tabular" label="${tool.name} on ${on_string}"/> + <data name="out_file_detail" format="tabular" label="${tool.name} on ${on_string}: Detailed SNPs file"> + <filter>tsv</filter> + </data> </outputs> <tests> <test expect_num_outputs="1"> @@ -107,6 +114,27 @@ </assert_contents> </output> </test> + <test expect_num_outputs="2"> + <param name="input_hal" value="halTestExtended.hal"/> + <param name="refGenome" value="Genome_0"/> + <param name="targetGenomes" value="Genome_1,Insert"/> + <param name="tsv" value="true"/> + <output name="out_file" ftype="tabular"> + <assert_contents> + <has_line line="targetGenome	totalSnps	totalCleanOrthologousPairs"/> + <has_line line="Genome_1	0	0"/> + <has_line line="Insert	32	586"/> + <has_n_lines n="3"/> + </assert_contents> + </output> + <output name="out_file_detail" ftype="tabular"> + <assert_contents> + <has_line line="refSequence	refPosition	Genome_0	Genome_1	Insert"/> + <has_line line="Genome_0_seq	10	G		C"/> + <has_n_lines n="33"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ halSnps counts SNPs between orthologous positions across multiple genomes in a HAL alignment.
--- a/macros.xml Thu Mar 05 11:35:43 2026 +0000 +++ b/macros.xml Wed Mar 18 15:21:28 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="@VERSION_SUFFIX@">1</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>