diff hyphy_bgm.xml @ 23:ede53272264e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"

--- a/hyphy_bgm.xml	Fri Apr 09 21:52:50 2021 +0000
+++ b/hyphy_bgm.xml	Tue Apr 20 10:33:00 2021 +0000
@@ -3,14 +3,17 @@
     <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[
-        ln -s '$input_file' bgm_input.fa &&
-        ln -s '$input_nhx' bgm_input.nhx &&
+        @SYMLINK_FILES@
         hyphy bgm
-            --alignment ./bgm_input.fa
-            --tree ./bgm_input.nhx
+            --alignment ./$input_file
+            #if $input_nhx:
+                --tree ./input.nhx
+            #end if
             --run_type $datatype.value
             #if $datatype.value == "codon":
                 --code '$datatype.gencodeid'
@@ -24,11 +27,11 @@
             --samples '$samples'
             --parents '$parents'
             --min_subs '$min_subs'
-            > '$bgm_log'
+            > '$bgm_log' ;
+        @CATCH_ERROR@
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
-        <param name="input_nhx" type="data" format="nhx" label="Input newick file"/>
+        <expand macro="inputs" />
         <conditional name="datatype">
             <param name="value" type="select" label="Type of data">
                 <option value="nucleotide">Nucleotide</option>