diff hyphy_prime.xml @ 17:6d29207a32c5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"

--- a/hyphy_prime.xml	Tue Apr 20 19:54:11 2021 +0000
+++ b/hyphy_prime.xml	Tue Apr 27 18:04:23 2021 +0000
@@ -1,27 +1,22 @@
 <?xml version="1.0"?>
-<tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_prime" name="HyPhy-PRIME" version="@VERSION@+galaxy1" profile="19.09">
     <description>Property Informed Models of Evolution</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">PRIME</token>
-        <token name="@operation@">prime</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
         @HYPHYMPI@ prime
             --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
+            @INPUT_TREE@
             --code '$gencodeid'
-            --branches '$branches'
+            @branch_options@
             --pvalue '$p_value'
             --properties '$prop_set'
+            --impute-states '$impute_states'
             --output '$prime_output'
-            > '$prime_log'
-            ;
-        @CATCH_ERROR@
+        @ERRORS@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -32,9 +27,9 @@
             <option value="LCAP">LCAP</option>
         </param>
         <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
+        <param argument="--impute-states" type="boolean" truevalue="Yes" falsevalue="No" label="Use site-level model fits to impute likely character states for each sequence"/>
     </inputs>
     <outputs>
-        <data name="prime_log" format="txt"/>
         <data name="prime_output" format="hyphy_results.json" />
     </outputs>
     <tests>