diff rnaz.xml @ 2:580ee1e91801 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rnaz commit e85474d72b07c70ca061f51b7165951038a06a6c

--- a/rnaz.xml	Wed Mar 01 17:15:13 2017 -0500
+++ b/rnaz.xml	Thu Sep 28 11:21:09 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="rnaz" name="RNAz" version="2.1.0">
+<tool id="rnaz" name="RNAz" version="2.1.1">
     <description>predicting structurally conserved and thermodynamically stable RNA secondary structures</description>
 
     <requirements>
@@ -15,8 +15,7 @@
 <![CDATA[
     RNAz '$input'
         --$forward_or_reverse
-        $dinucleotide
-        $mononucleotide
+        $zscore
         $locarnate
         $noshuffle
         #if $cutoff != -1.0:
@@ -34,9 +33,11 @@
             <option value="reverse">Score reverse strand (-r)</option>
             <option value="both-strands">Score both strands (-b)</option>
         </param>
+        <param name="zscore" type="select" label="Which type of z-scores">
+            <option value="--mononucleotide">Use mononucleotide shuffled z-scores</option>
+            <option value="--dinucleotide" selected="true">Use dinucleotide shuffled z-scores</option>
+        </param>
         <param argument="--cutoff" label="Probability cutoff" type="float" value="-1.0" help="-1.0 to deactivate"/>
-        <param argument="--dinucleotide" type="boolean" checked="true" truevalue="--dinucleotide" falsevalue="" label="Use dinucleotide shuffled z-scores" />
-        <param argument="--mononucleotide" type="boolean" checked="true" truevalue="--mononucleotide" falsevalue="" label="Use mononucleotide shuffled z-scores"  />
         <param argument="--locarnate" type="boolean" checked="false" truevalue="--locarnate" falsevalue="" label="Use decision model for structural alignments" />
         <param argument="--no-shuffle" name="noshuffle"  type="boolean" checked="false" truevalue="--no-shuffle" falsevalue="" label="Never fall back to shuffling"  />
     </inputs>