# HG changeset patch
# User iuc
# Date 1516728000 18000
# Node ID fcc6efc4ef6d2762f2c7becf90c0f75463ab309f
# Parent  7f9d1892eb1bae2236c8fa4361eb6d29ea4679bd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 1912a560c3ad87117f18570fcf3ba4af4f924340

diff -r 7f9d1892eb1b -r fcc6efc4ef6d bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Sat Jan 20 08:22:03 2018 -0500
+++ b/bowtie2_wrapper.xml	Tue Jan 23 12:20:00 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bowtie2" name="Bowtie2" version="2.3.4" profile="17.01">
+<tool id="bowtie2" name="Bowtie2" version="2.3.4.1" profile="17.01">
     <description>- map reads against reference genome</description>
     <macros>
         <import>bowtie2_macros.xml</import>
@@ -282,9 +282,9 @@
     #if str( $analysis_type.sam_options.sam_options_selector ) == "yes":
         ${analysis_type.sam_options.no_unal}
         ${analysis_type.sam_options.omit_sec_seq}
-        ${analysis_type.sam_options.sam-no-qname-trunc}
+        ${analysis_type.sam_options.sam_no_qname_trunc}
         ${analysis_type.sam_options.xeq}
-        ${analysis_type.sam_options.soft-clipped-unmapped-tlen}
+        ${analysis_type.sam_options.soft_clipped_unmapped_tlen}
     #end if
 
     #if str( $analysis_type.other_options.other_options_selector ) == "yes":
@@ -503,9 +503,9 @@
                     <when value="yes">
                         <param name="no_unal" type="boolean" truevalue="--no-unal" falsevalue="" label="Suppress SAM records for reads that failed to align" help="--no-unal; Default=False"/>
                         <param name="omit_sec_seq" type="boolean" truevalue="--omit-sec-seq" falsevalue="" label="Suppress SEQ and QUAL strings for secondary alignments" help="--omit-sec-seq; Default=False"/>
-                        <param argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
+                        <param name="sam_no_qname_trunc" argument="--sam-no-qname-trunc" type="boolean" truevalue="--sam-no-qname-trunc" falsevalue="" label="Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM"/>
                         <param argument="--xeq" type="boolean" truevalue="--xeq" falsevalue="" label="Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record."/>
-                        <param argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
+                        <param name="soft_clipped_unmapped_tlen" argument="--soft-clipped-unmapped-tlen" type="boolean" truevalue="--soft-clipped-unmapped-tlen" falsevalue="" label=" Exclude soft-clipped bases when reporting TLEN"/>
                     </when>
                     <when value="no">
                         <!-- do nothing -->