diff hyphy_gard.xml @ 23:a0731e81e0c2 draft

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

--- a/hyphy_gard.xml	Fri Apr 09 21:48:33 2021 +0000
+++ b/hyphy_gard.xml	Tue Apr 20 10:25:18 2021 +0000
@@ -3,12 +3,15 @@
     <description>Genetic Algorithm for Recombination Detection</description>
     <macros>
         <import>macros.xml</import>
+        <token name="@OPERATION@">GARD</token>
+        <token name="@operation@">gard</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_file' gard_input.fa &&
+        ln -s '$input_file' input.$input_file.extension &&
+        #set $input_file = 'input.%s' % $input_file.extension
         @HYPHYMPI@ gard
-            --alignment ./gard_input.fa
+            --alignment ./$input_file
             --type '$datatype.value'
             #if str($datatype.value) == 'codon':
                 --code '$datatype.gencodeid'
@@ -23,10 +26,10 @@
             --output-lf '$gard_output'
             > '$gard_log'
             ;
-        @CATCH_MPIERR@
+        @CATCH_ERROR@
     ]]></command>
     <inputs>
-        <param name="input_file" type="data" format="fasta" label="Input FASTA file"/>
+        <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" />
         <conditional name="datatype">
             <param argument="--type" name="value" type="select" label="Alignment kind">
                 <option value="nucleotide">Nucleotide</option>
@@ -64,7 +67,7 @@
     <tests>
         <test>
             <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
-            <output name="gard_output" file="gard-out1.nex" compare="sim_size" delta="160000"/>
+            <output name="gard_output" file="gard-out1.nex" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[