# HG changeset patch
# User iuc
# Date 1566581041 14400
# Node ID 739b008acace0d705d10eda998d4b1e62808994d
# Parent  cd8b7d755af855c5d818769b0b4aebbec1a8df57
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit be3590f33762e4797eaa1462d495e8e8a1b98110"

diff -r cd8b7d755af8 -r 739b008acace bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Thu Apr 04 09:39:19 2019 -0400
+++ b/bowtie2_wrapper.xml	Fri Aug 23 13:24:01 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="bowtie2" name="Bowtie2" version="2.3.4.3" profile="18.01">
+<tool id="bowtie2" name="Bowtie2" version="2.3.4.3+galaxy0" profile="18.01">
     <description>- map reads against reference genome</description>
     <macros>
         <import>bowtie2_macros.xml</import>
@@ -281,7 +281,6 @@
         -R ${analysis_type.effort_options.R}
     #end if
     #if str( $analysis_type.other_options.other_options_selector ) == "yes":
-        ${analysis_type.other_options.reorder}
         ${analysis_type.other_options.non_deterministic}
         --seed ${analysis_type.other_options.seed}
     #end if
@@ -314,13 +313,13 @@
 #end if
 
 ## rename unaligned sequence files
-#if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
+#if ($library.type == "paired" or $library.type == "paired_collection") and $output_unaligned_reads_l and $output_unaligned_reads_r:
     #from os.path import splitext
     #set _unaligned_root, _unaligned_ext = splitext( str( $output_unaligned_reads_l ) )
     && mv '${ _unaligned_root }.1${_unaligned_ext}' '$output_unaligned_reads_l'
     && mv '${ _unaligned_root }.2${_unaligned_ext}' '$output_unaligned_reads_r'
 #end if
-#if $library.type == "paired" and $output_aligned_reads_l and $output_aligned_reads_r:
+#if ($library.type == "paired" or $library.type == "paired_collection") and $output_aligned_reads_l and $output_aligned_reads_r:
     #from os.path import splitext
     #set _aligned_root, _aligned_ext = splitext( str( $output_aligned_reads_l ) )
     && mv '${ _aligned_root }.1${_aligned_ext}' '$output_aligned_reads_l'
@@ -505,7 +504,6 @@
                         <option value="no" selected="true">No</option>
                     </param>
                     <when value="yes">
-                        <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" label="Guarantee that output SAM records are printed in an order corresponding to the order of the reads in the original input file. If selected output file will not be coordinate sorted." help="--reorder; Default=False"/>
                         <param name="seed" type="integer" value="0" min="0" label="Use this number as the seed for pseudo-random number generator" help="--seed; Default=0"/>
                         <param name="non_deterministic" type="boolean" truevalue="--non-deterministic" falsevalue="" label="Re-initialize the pseudo-random generator for each read using the current time" help="--non-deterministic; see Help below for explanation of this option; default=False"/>
                     </when>
@@ -663,11 +661,11 @@
             <param name="own_file" value="bowtie2-ref.fasta" />
             <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
         </test>
-        <test expect_num_outputs="1">
-            <!-- test on paired collection -->
+        <test expect_num_outputs="3">
+            <!-- test on list paired collection -->
             <param name="type" value="paired_collection"/>
             <param name="paired_options_selector" value="no"/>
-            <param name="unaligned_file" value="false"/>
+            <param name="unaligned_file" value="true"/>
             <param name="analysis_type_selector" value="simple"/>
             <param name="source" value="history" />
             <param name="input_1">