# HG changeset patch
# User iuc
# Date 1510655312 18000
# Node ID 6f718d3182d7f2d644a648df4b19aaf912f9708c
# Parent  a537774e1979fb511546deae100c89410943c149
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 7b3489c9010a339e83beb1f40044bd145cab967a

diff -r a537774e1979 -r 6f718d3182d7 hisat2.xml
--- a/hisat2.xml	Sat Sep 30 04:43:01 2017 -0400
+++ b/hisat2.xml	Tue Nov 14 05:28:32 2017 -0500
@@ -469,8 +469,8 @@
                     <param name="max_intron" type="integer" value="500000" min="0" label="Maximum intron length" />
                     <conditional name="no_spliced_alignment_options">
                         <param name="no_spliced_alignment" argument="--no-spliced-alignment" type="select" label="Disable spliced alignment">
+                            <option value="">False</option>
                             <option value="--no-spliced-alignment">True</option>
-                            <option value="">False</option>
                         </param>
                         <when value="--no-spliced-alignment">
                             <param name="minins" argument="-I" type="integer" value="0" min="0" label="Minimum fragment length for valid paired-end alignments" help="E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates. The larger the difference between -I and -X, the slower HISAT2 will run. This is because larger differences between -I and -X require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient" />
@@ -480,10 +480,10 @@
                     </conditional>
                     <param name="known_splice_gtf" type="data" format="gtf" optional="true" label="GTF file with known splice sites" />
                     <param name="tma" type="select" display="radio" label="Transcriptome assembly reporting">
-                        <option value="">Use default reporting.</option>
-                        <option value="--tmo">Report only those alignments within known transcripts.</option>
-                        <option value="--dta">Report alignments tailored for transcript assemblers including StringTie.</option>
-                        <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks.</option>
+                        <option value="">Use default reporting</option>
+                        <option value="--tmo">Report only those alignments within known transcripts</option>
+                        <option value="--dta">Report alignments tailored for transcript assemblers including StringTie</option>
+                        <option value="--dta-cufflinks">Report alignments tailored specifically for Cufflinks</option>
                     </param>
                     <param name="notmplen" argument="--no-templatelen-adjustment" type="boolean" truevalue="--no-templatelen-adjustment" falsevalue="" label="Disable automatic template length adjustment for RNA-seq reads" help="Default: false" />
                 </when>