# HG changeset patch
# User iuc
# Date 1452846791 18000
# Node ID c37b4554f794a16c5f30aeeadeaf0a59baeb2a5a
# Parent  6d4d39720545b5d6f3e156110012ad55f72e8dd3
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit a2aaa7c9fe7b343f95450ec428250317696a9fb7

diff -r 6d4d39720545 -r c37b4554f794 hisat2.xml
--- a/hisat2.xml	Sat Oct 10 16:24:47 2015 -0400
+++ b/hisat2.xml	Fri Jan 15 03:33:11 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hisat2" name="HISAT2" version="1.0.0">
+<tool id="hisat2" name="HISAT2" version="1.0.1">
     <description>A fast and sensitive alignment program</description>
     <macros>
         <import>hisat2_macros.xml</import>
@@ -61,7 +61,7 @@
         #end if
         #if str($alignment_options.alignment_options_selector) == "advanced":
             --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient}
-            ${alignment_options.skip_forward} ${alignment_options.skip_reverse}
+            ${alignment_options.skip_forward} ${alignment_options.skip_reverse} ${alignment_options.ignore_quals}
         #end if
         #if str($spliced_options.spliced_options_selector) == "advanced":
             --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}
@@ -193,7 +193,7 @@
                     <option value="R">First Strand (R/RF)</option>
                     <option value="F">Second Strand (F/FR)</option>
                 </param>
-                <param argument="--no-spliced-alignment" name="ignore_quals" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" />
+                <param argument="--no-spliced-alignment" name="no_spliced_alignment" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" />
                 <param format="gtf" label="GTF file with known splice sites" name="known_splice_gtf" optional="True" type="data" />
                 <param display="radio" label="Transcriptome assembly reporting" name="tma" type="select">
                     <option value="">Use default reporting.</option>
diff -r 6d4d39720545 -r c37b4554f794 hisat2_macros.xml
--- a/hisat2_macros.xml	Sat Oct 10 16:24:47 2015 -0400
+++ b/hisat2_macros.xml	Fri Jan 15 03:33:11 2016 -0500
@@ -25,12 +25,12 @@
                 <expand macro="paired_end_conditional" />
             </when>
             <when value="paired">
-                <param format="@FTYPE@" label="Forward reads" multiple="true" name="reads_f" type="data" />
-                <param format="@FTYPE@" label="Reverse reads" multiple="true" name="reads_r" type="data" />
+                <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" />
+                <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" />
                 <expand macro="paired_end_conditional" />
             </when>
             <when value="single">
-                <param format="@FTYPE@" label="Reads" multiple="true" name="reads" type="data" />
+                <param format="@FTYPE@" label="Reads" name="reads" type="data" />
             </when>
         </conditional>
     </xml>
@@ -56,7 +56,7 @@
             ${input_format.paired.paired_end_options.no_discordant}
         #end if
     </token>
-    <token name="strandedness_parameters">
+    <token name="@strandedness_parameters@">
         #if str($spliced_options.spliced_options_selector) == "advanced":
             #if str($spliced_options.rna_strandness).strip() != '':
                 --rna-strandness $spliced_options.rna_strandness