diff hyphy_bgm.xml @ 25:d88bbb287923 draft

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

--- a/hyphy_bgm.xml	Tue Apr 20 19:56:21 2021 +0000
+++ b/hyphy_bgm.xml	Tue Apr 27 18:01:09 2021 +0000
@@ -1,19 +1,15 @@
 <?xml version="1.0"?>
-<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_bgm" name="HyPhy-BGM" version="@VERSION@+galaxy1" profile="19.09">
     <description>- Detecting coevolving sites via Bayesian graphical models</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">BGM</token>
-        <token name="@operation@">bgm</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
         hyphy bgm
             --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
+            @INPUT_TREE@
             --run_type $datatype.value
             #if $datatype.value == "codon":
                 --code '$datatype.gencodeid'
@@ -21,14 +17,13 @@
             #if $datatype.value == "protein":
                 --baseline_model '$datatype.model'
             #end if
-            --branches '$branches'
+            @branch_options@
             --chain '$chain_length'
             --burn_in '$burn_in'
             --samples '$samples'
             --parents '$parents'
             --min_subs '$min_subs'
-            > '$bgm_log' ;
-        @CATCH_ERROR@
+        @ERRORS@
     ]]></command>
     <inputs>
         <expand macro="inputs" />
@@ -54,7 +49,6 @@
         <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_log" format="txt"/>
         <data name="bgm_output" format="hyphy_results.json" from_work_dir="bgm_input.fa.BGM.json"/>
     </outputs>
     <tests>