diff -r 6d4d39720545 hisat2.xml

--- a/hisat2.xml Sat Oct 10 16:24:47 2015 -0400

+++ b/hisat2.xml Thu Dec 10 17:07:38 2015 -0500

@@ -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 hisat2_macros.xml

--- a/hisat2_macros.xml Sat Oct 10 16:24:47 2015 -0400

+++ b/hisat2_macros.xml Thu Dec 10 17:07:38 2015 -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="fastqsanger" label="Forward reads" multiple="true" name="reads_f" type="data" />

+                <param format="fastqsanger" label="Reverse reads" multiple="true" 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="fastqsanger" label="Reads" multiple="true" 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