Mercurial > repos > iuc > hyphy_fade

diff hyphy_fade.xml @ 25:5e8d0e777033 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:06:34 +0000
parents 17ac281a46d9
children 96817f0fd28b
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line diff
--- a/hyphy_fade.xml	Tue Apr 20 19:49:45 2021 +0000
+++ b/hyphy_fade.xml	Tue Apr 27 18:06:34 2021 +0000
@@ -1,29 +1,24 @@
 <?xml version="1.0"?>
-<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_fade" name="HyPhy-FADE" version="@VERSION@+galaxy1" profile="19.09">
     <description>: FUBAR* Approach to Directional Evolution (*Fast
     Unconstrained Bayesian Approximation)</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">FADE</token>
-        <token name="@operation@">fade</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
         hyphy fade
-            --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
-            --branches '$branches'
+            --alignment $input_file
+            @INPUT_TREE@
+            @branch_options@
             --model '$model'
             --method '$posteriorEstimationMethod.method'
             --grid '$grid_points'
             --concentration_parameter '$concentration'
             @posteriorEstimationMethod_cmd@
             --output '$fade_output'
-            > '$fade_log' ;
-        @CATCH_ERROR@
+        @ERRORS@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -35,7 +30,6 @@
         <param name="concentration" type="float" value="0.5" min="0.001" max="1" label="Concentration parameter of the Dirichlet prior"/>
     </inputs>
     <outputs>
-        <data name="fade_log" format="txt"/>
         <data name="fade_output" format="hyphy_results.json" />
     </outputs>
     <tests>