diff hyphy_fade.xml @ 23:17ac281a46d9 draft

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

--- a/hyphy_fade.xml	Fri Apr 09 21:49:02 2021 +0000
+++ b/hyphy_fade.xml	Tue Apr 20 10:25:54 2021 +0000
@@ -4,14 +4,17 @@
     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[
-        ln -s '$input_file' fade_input.fa &&
-        ln -s '$input_nhx' fade_input.nhx &&
+        @SYMLINK_FILES@
         hyphy fade
-            --alignment ./fade_input.fa
-            --tree ./fade_input.nhx
+            --alignment ./$input_file
+            #if $input_nhx:
+                --tree ./input.nhx
+            #end if
             --branches '$branches'
             --model '$model'
             --method '$posteriorEstimationMethod.method'
@@ -19,11 +22,11 @@
             --concentration_parameter '$concentration'
             @posteriorEstimationMethod_cmd@
             --output '$fade_output'
-            > '$fade_log'
+            > '$fade_log' ;
+        @CATCH_ERROR@
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="fasta" label="Input amino acid FASTA file"/>
-        <param name="input_nhx" type="data" format="nhx" label="Input rooted newick file"/>
+        <expand macro="inputs"/>
         <expand macro="branches"/>
         <expand macro="substitution"/>
         <expand macro="branches"/>