diff hyphy_fel.xml @ 33:8a6ef85b934d draft

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

--- a/hyphy_fel.xml	Sat Nov 27 11:31:22 2021 +0000
+++ b/hyphy_fel.xml	Wed Mar 30 00:12:04 2022 +0000
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool id="hyphy_fel" name="HyPhy-FEL" version="@TOOL_VERSION@+galaxy1" profile="19.09">
     <description>Fixed 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@
@@ -15,6 +15,9 @@
             @branch_options@
             --srv '$include_srv'
             --pvalue '$p_value'
+            @resample@
+            --precision $precision
+            $ci
             --output '$fel_output'
         @ERRORS@
     ]]></command>
@@ -27,6 +30,12 @@
             <option value="Yes">Yes (recommended)</option>
             <option value="No">No</option>
         </param>
+        <param argument="--ci" type="boolean" truevalue="--ci Yes" falsevalue="" label="Compute profile likelihood confidence intervals for each variable site" />
+        <expand macro="resample"/>
+        <param argument="--precision" type="select" label="Optimization precision for preliminary fits">
+            <option value="standard">Standard</option>
+            <option value="reduced">Reduced for faster fitting</option>
+        </param>
     </inputs>
     <outputs>
         <data name="fel_output" format="hyphy_results.json" />
@@ -37,6 +46,13 @@
             <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
             <output name="fel_output" file="fel-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="ci" value="true" />
+            <param name="precision" value="reduced" />
+            <output name="fel_output" file="fel-out1.json" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 FEL : Fixed effects likelihood