diff hyphy_absrel.xml @ 16:4cc4dbca2f02 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"

--- a/hyphy_absrel.xml	Fri Aug 21 15:24:17 2020 -0400
+++ b/hyphy_absrel.xml	Fri Sep 18 21:10:47 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
+<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1">
     <description>adaptive Branch Site Random Effects Likelihood</description>
     <macros>
         <import>macros.xml</import>
@@ -14,6 +14,7 @@
             --code '$gencodeid'
             --branches '$branches'
             --output '$absrel_output'
+            --multiple-hits $multiple_hits
             #if $log:
                 > '$absrel_log'
             #end if
@@ -24,6 +25,11 @@
         <expand macro="inputs"/>
         <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
         <expand macro="gencode"/>
+        <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions">
+            <option value="None">Use standard models which permit only single nucleotide changes to occur instantly</option>
+            <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
+            <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
+        </param>
         <expand macro="branches"/>
     </inputs>
     <outputs>
@@ -36,6 +42,14 @@
         <test>
             <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
             <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
+            <param name="multiple_hits" value="None" />
+            <param name="log" value="false"/>
+            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
+            <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
+            <param name="multiple_hits" value="Double" />
             <param name="log" value="false"/>
             <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
         </test>