# HG changeset patch
# User iuc
# Date 1478689055 18000
# Node ID 5f4da9ec47c79eb16b0a07c6e1960ed0058a9cc2
# Parent  1eb21dccc2fa9fe59f26994c573c629adfcb9bb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit bfa8bda732de882f6fa5f5375f8468ad229cceea

diff -r 1eb21dccc2fa -r 5f4da9ec47c7 hisat2.xml
--- a/hisat2.xml	Thu Jun 02 11:02:23 2016 -0400
+++ b/hisat2.xml	Wed Nov 09 05:57:35 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" />