Mercurial > repos > iuc > hyphy_gard

diff hyphy_gard.xml @ 25:1fb98a84e86d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
author iuc
date Tue, 27 Apr 2021 18:05:30 +0000
parents a0731e81e0c2
children 45d39a499816
line wrap: on
line diff
--- a/hyphy_gard.xml	Tue Apr 20 19:49:13 2021 +0000
+++ b/hyphy_gard.xml	Tue Apr 27 18:05:30 2021 +0000
@@ -1,10 +1,8 @@
 <?xml version="1.0"?>
-<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_gard" name="HyPhy-GARD" version="@VERSION@+galaxy1" profile="19.09">
     <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[
@@ -20,13 +18,11 @@
             #end if
             #if str($rate_cond.rate):
                 --rv '$rate_cond.rate'
-                --rate-classes '$rate_classes'
+                --rate-classes '$rate_cond.rate_classes'
             #end if
             --output '$translated'
             --output-lf '$gard_output'
-            > '$gard_log'
-            ;
-        @CATCH_ERROR@
+        @ERRORS@
     ]]></command>
     <inputs>
         <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" />
@@ -52,15 +48,14 @@
             </param>
             <when value=""/>
             <when value="GDD">
-                <param argument="--rate-classes" name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
+                <param argument="--rate-classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
             </when>
             <when value="Gamma">
-                <param argument="--rate-classes" name="rate_classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
+                <param argument="--rate-classes" type="integer" value="2" min="2" max="6" label="Rate classes" />
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data name="gard_log" format="txt"/>
         <data name="gard_output" format="nex" />
         <data name="translated" format="hyphy_results.json" />
     </outputs>
@@ -68,6 +63,7 @@
         <test>
             <param name="input_file" ftype="fasta" value="gard-in1.fa"/>
             <output name="gard_output" file="gard-out1.nex" compare="sim_size"/>
+            <output name="translated" file="gard-out1.json" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[