# HG changeset patch
# User iuc
# Date 1478691021 18000
# Node ID 98c2e5bd2407d5b2e258fe05d2bc9fa328fd815d
# Parent  8979161ef72c5e30dd68820cbebfdafdf307581f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit bfa8bda732de882f6fa5f5375f8468ad229cceea

diff -r 8979161ef72c -r 98c2e5bd2407 hisat2.xml
--- a/hisat2.xml	Thu Jun 02 11:02:11 2016 -0400
+++ b/hisat2.xml	Wed Nov 09 06:30:21 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hisat2" name="HISAT" version="2.0.3">
+<tool id="hisat2" name="HISAT" version="2.0.3.1">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -89,7 +89,7 @@
     <inputs>
         <conditional name="input_format">
             <param label="Input data format" name="input_format_selector" type="select">
-                <option selected="selected" value="fastq">FASTQ</option>
+                <option selected="true" value="fastq">FASTQ</option>
                 <option value="fasta">FASTA</option>
             </param>
             <when value="fasta">
@@ -113,7 +113,7 @@
                 </param>
             </when>
             <when value="history">
-                <param format="fasta" label="Select the reference genome" metadata_name="dbkey" name="history_item" type="data" />
+                <param format="fasta" label="Select the reference genome" name="history_item" type="data" />
             </when>
         </conditional>
         <param argument="-k" name="max_primary" optional="True" type="integer" value="5" help="Search for at most K distinct, primary alignments for each read. Primary alignments mean alignments whose alignment score is equal or higher than any other alignments. The search terminates when it can't find more distinct valid alignments, or when it finds K, whichever happens first." label="Primary alignments" />
@@ -184,7 +184,7 @@
                     <option value="C">Constant</option>
                     <option value="L">Linear [f(x) = y + z * x]</option>
                     <option value="S">Square root [f(x) = y + z * x&#178;]</option>
-                    <option selected="selected" value="G">Natural logarithm [f(x) = y + z * log(x)]</option>
+                    <option selected="True" value="G">Natural logarithm [f(x) = y + z * log(x)]</option>
                 </param>
                 <param help="Constant term for long non-canonical introns" label="Constant term (y)" name="nc_constant_term" type="integer" value="-8" />
                 <param help="Coefficient for long non-canonical introns" label="Coefficient (z)" name="nc_coefficient" type="integer" value="1" />