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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs commit be65e1846c9d4d63e80c01625e6e5f0d613948fe |
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modified:
yahs.xml |
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| diff -r 39495e107274 -r 425e63adcc5d yahs.xml --- a/yahs.xml Wed Sep 28 09:41:02 2022 +0000 +++ b/yahs.xml Thu Mar 09 21:59:34 2023 +0000 |
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| @@ -2,7 +2,7 @@ <description>yet another HI-C scaffolding tool</description> <macros> <token name="@VERSION@">1.2a.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@VERSION@">yahs</requirement> @@ -39,8 +39,10 @@ -e 'GATC' #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima1' -e 'GATC,GANTC' - #else + #else if $function.enzyme_conditional.preconfigured_enzymes == 'arima2' -e 'GATC,GANTC,CTNAG,TTAA' + #else if $function.enzyme_conditional.preconfigured_enzymes == 'omnic' + #end if #else if $function.enzyme_conditional.enzyme_options == 'specific': -e '${function.enzyme_conditional.manual_enzyme}' @@ -101,6 +103,7 @@ <option value="dovetail">Dovetail Chicago, Dovetail Hi-C or Phase: GATC</option> <option value="arima1">Arima Hi-C 1.0: GATC, GANTC</option> <option value="arima2">Arima Hi-C 2.0: GATC, GANTC, CTNAG, TTAA</option> + <option value="omnic">Dovetail Omni-C: enzyme-free prep</option> </param> </when> <when value="specific"> @@ -248,6 +251,24 @@ </output> <!-- COMMAND: yahs test.fasta test.bed -r 50000,100000,150000,2000000,1000000 -a test.agp -o test_1 --> </test> + <!-- TEST 7: omnic prep --> + <test expect_num_outputs="6"> + <conditional name="function"> + <param name="function_select" value="yahs"/> + <param name="fasta" value="test.fasta"/> + <param name="bfile" value="test.bed"/> + </conditional> + <conditional name="enzyme_conditional"> + <param name="enzyme_options" value="preconfigured"/> + <param name="preconfigured_enzymes" value="omnic"/> + </conditional> + <param name="log_out" value="yes"/> + <output name="log_file" ftype="txt"> + <assert_contents> + <not_has_text text="-e"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ YaHS is scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies. YaHS has been tested in a wide range of genome assemblies. Compared to other Hi-C scaffolding tools, it usually generates more contiguous scaffolds - especially with a higher N90 and L90 statistics. It is also super fast - takes less than 5 minutes to reconstruct the human genome from an assembly of 5,483 contigs with ~45X Hi-C data. |