Mercurial > repos > iuc > hyphy_slac

diff hyphy_slac.xml @ 26:0c6724c345d9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:00:01 +0000
parents ec499ddce7a9
children c010cbc8ff3a
line wrap: on
line diff
--- a/hyphy_slac.xml	Tue Apr 20 19:52:29 2021 +0000
+++ b/hyphy_slac.xml	Tue Apr 27 18:00:01 2021 +0000
@@ -1,26 +1,21 @@
 <?xml version="1.0"?>
-<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_slac" name="HyPhy-SLAC" version="@VERSION@+galaxy1" profile="19.09">
     <description>Single Likelihood Ancestor Counting</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">SLAC</token>
-        <token name="@operation@">slac</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
         hyphy slac
             --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
+            @INPUT_TREE@
             --code '$gencodeid'
-            --branches '$branches'
+            @branch_options@
             --samples '$number_of_samples'
             --pvalue '$p_value'
             --output '$slac_output'
-        > '$slac_log' ;
-        @CATCH_ERROR@
+        @ERRORS@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -30,7 +25,6 @@
         <param argument="--samples" name="number_of_samples" type="integer" value="100" min="0" max="100000" label="Number of samples used to assess ancestral reconstruction uncertainty"/>
     </inputs>
     <outputs>
-        <data name="slac_log" format="txt"/>
         <data name="slac_output" format="hyphy_results.json" />
     </outputs>
     <tests>