diff hyphy_absrel.xml @ 35:841557158611 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954

--- a/hyphy_absrel.xml	Thu Aug 18 14:05:48 2022 +0000
+++ b/hyphy_absrel.xml	Thu Mar 02 15:09:44 2023 +0000
@@ -1,5 +1,4 @@
-<?xml version="1.0"?>
-<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy2" profile="19.09">
+<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>adaptive Branch Site Random Effects Likelihood</description>
     <macros>
         <import>macros.xml</import>
@@ -22,7 +21,7 @@
     <inputs>
         <expand macro="inputs"/>
         <expand macro="gencode"/>
-        <param name="multiple_hits" type="select" argument="--multiple-hits" label="Include support for multiple nucleotide substitutions">
+        <param argument="--multiple-hits" type="select" 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>
@@ -38,20 +37,50 @@
             <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" />
-            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
+            <output name="absrel_output">
+                <assert_contents>
+                    <has_size value="10512" delta="100"/>
+                    <has_text text="fits"/>
+                    <has_text text="branch attributes"/>
+                    <has_text text="Full adaptive model"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="found **2** branches under selection among **5** tested"/>
+            </assert_stdout>
         </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" />
-            <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
+            <output name="absrel_output">
+                <assert_contents>
+                    <has_size value="11117" delta="100"/>
+                    <has_text text="fits"/>
+                    <has_text text="branch attributes"/>
+                    <has_text text="Full adaptive model"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="found **0** branches under selection among **5** tested"/>
+            </assert_stdout>
         </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"/>
+            <param name="srv" value="true" />
+            <output name="absrel_output">
+                <assert_contents>
+                    <has_size value="23396" delta="100"/>
+                    <has_text text="fits"/>
+                    <has_text text="branch attributes"/>
+                    <has_text text="Full adaptive model"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_text text="found **0** branches under selection among **5** tested"/>
+            </assert_stdout>
         </test>
     </tests>
     <help><![CDATA[