# HG changeset patch
# User iuc
# Date 1621368543 0
# Node ID d1c977aee22869186f0a11a27b698224757eab04
# Parent  d88bbb287923991efd1fbb44c5ee36be166e6380
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2dd9bdc695433c217bbb7e11c1c0138245beb801"

diff -r d88bbb287923 -r d1c977aee228 hyphy_bgm.xml
--- a/hyphy_bgm.xml	Tue Apr 27 18:01:09 2021 +0000
+++ b/hyphy_bgm.xml	Tue May 18 20:09:03 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy1" profile="19.09">
+<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy2" profile="19.09">
     <description>- Detecting coevolving sites via Bayesian graphical models</description>
     <macros>
         <import>macros.xml</import>
@@ -7,8 +7,9 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
+        ln -s '$bgm_output' ${input_file}.BGM.json &&
         hyphy bgm
-            --alignment ./$input_file
+            --alignment $input_file
             @INPUT_TREE@
             --run_type $datatype.value
             #if $datatype.value == "codon":
@@ -49,7 +50,7 @@
         <param argument="--min-subs" name="min_subs" type="integer" value="1" min="1" max="100000" label="Minimum number of ubstitutions per site to be included in the analysis" />
     </inputs>
     <outputs>
-        <data name="bgm_output" format="hyphy_results.json" from_work_dir="bgm_input.fa.BGM.json"/>
+        <data name="bgm_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>