Mercurial > repos > iuc > hyphy_bgm
diff hyphy_bgm.xml @ 35:35723f87964d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
| author | iuc |
|---|---|
| date | Thu, 02 Mar 2023 15:13:13 +0000 |
| parents | 5b6b8b08f1a9 |
| children |
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--- a/hyphy_bgm.xml Thu Aug 18 14:01:09 2022 +0000 +++ b/hyphy_bgm.xml Thu Mar 02 15:13:13 2023 +0000 @@ -1,5 +1,4 @@ -<?xml version="1.0"?> -<tool id="hyphy_bgm" name="HyPhy-BGM" version="@TOOL_VERSION@+galaxy2" profile="19.09"> +<tool id="hyphy_bgm" name="HyPhy-BGM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- Detecting coevolving sites via Bayesian graphical models</description> <macros> <import>macros.xml</import> @@ -17,7 +16,7 @@ --code '$datatype.gencodeid' #end if #if $datatype.value == "protein": - --baseline_model '$datatype.model' + --baseline_model '$datatype.baseline_model' #end if @branch_options@ --chain '$chain_length' @@ -37,18 +36,18 @@ </param> <when value="nucleotide"/> <when value="amino-acid"> - <expand macro="substitution" /> + <expand macro="substitution" argument="--baseline_model" /> </when> <when value="codon"> <expand macro="gencode" /> </when> </conditional> <expand macro="branches"/> - <param name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/> - <param name="burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/> - <param name="samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/> + <param argument="--chain" name="chain_length" type="integer" value="100000" min="0" max="1000000000" label="Length of MCMC chain"/> + <param argument="--burn_in" type="integer" value="10000" min="0" max="1000000000" label="Number of samples to discard for burn-in"/> + <param argument="--samples" type="integer" value="100" min="0" max="100" label="Number of steps to extract from chain sample"/> <param argument="--max-parents" name="parents" type="integer" value="1" min="1" max="3" label="Maximum number of parents allowed per node" /> - <param argument="--min-subs" name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis" /> + <param argument="--min-subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis" /> </inputs> <outputs> <data name="bgm_output" format="hyphy_results.json" />