Mercurial > repos > iuc > hyphy_bgm

diff hyphy_bgm.xml @ 35:35723f87964d draft default tip

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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" />