diff hyphy_absrel.xml @ 33:212c958f6cee draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"

--- a/hyphy_absrel.xml	Sat Nov 27 11:25:19 2021 +0000
+++ b/hyphy_absrel.xml	Wed Mar 30 00:15:54 2022 +0000
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09">
     <description>adaptive Branch Site Random Effects Likelihood</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
@@ -16,6 +16,7 @@
             @branch_options@
             --output '$absrel_output'
             --multiple-hits $multiple_hits
+            $srv
         @ERRORS@
         ]]></command>
     <inputs>
@@ -26,6 +27,7 @@
             <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>
+        <param argument="--srv" type="boolean" truevalue="--srv Yes" falsevalue="" label="Include synonymous rate variation" />
         <expand macro="branches"/>
     </inputs>
     <outputs>
@@ -44,6 +46,13 @@
             <param name="multiple_hits" value="Double" />
             <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="srv" value="--srv Yes" />
+            <output name="absrel_output" file="absrel-out2.json" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[