# HG changeset patch
# User iuc
# Date 1643617873 0
# Node ID 2f3400246bfc69b5283bb90594ddfb452a22e2da
# Parent  56dcf3929d02fe4b956b747317e9ab023b7e61f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"

diff -r 56dcf3929d02 -r 2f3400246bfc bowtie2_macros.xml
--- a/bowtie2_macros.xml	Tue Aug 31 07:46:45 2021 +0000
+++ b/bowtie2_macros.xml	Mon Jan 31 08:31:13 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.4.2</token>
+    <token name="@TOOL_VERSION@">2.4.5</token>
     <!-- Import this at the top of your command block and then
          define rg_auto_name. -->
     <token name="@define_read_group_helpers@">
diff -r 56dcf3929d02 -r 2f3400246bfc bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Tue Aug 31 07:46:45 2021 +0000
+++ b/bowtie2_wrapper.xml	Mon Jan 31 08:31:13 2022 +0000
@@ -8,7 +8,7 @@
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
-        <requirement type="package" version="1.11">samtools</requirement>
+        <requirement type="package" version="1.14">samtools</requirement>
     </requirements>
     <version_command>bowtie2 --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -662,7 +662,7 @@
             <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
             <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
             <param name="own_file" value="bowtie2-ref.fasta" />
-            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test expect_num_outputs="3">
             <!-- test on list paired collection -->
@@ -678,7 +678,7 @@
                 </collection>
             </param>
             <param name="own_file" value="bowtie2-ref.fasta" />
-            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test expect_num_outputs="1">
             <!-- test on paired-end datasets with read group info -->
@@ -693,7 +693,7 @@
             <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
             <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
             <param name="own_file" value="bowtie2-ref.fasta" />
-            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test expect_num_outputs="2">
             <!-- test on paired-end datasets with stats output -->
@@ -706,7 +706,7 @@
             <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
             <param name="own_file" value="bowtie2-ref.fasta" />
             <param name="save_mapping_stats" value="true" />
-            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
             <output name="mapping_stats">
                 <assert_contents>
                     <has_text text="of these" />
@@ -725,7 +725,7 @@
             <param name="source" value="history" />
             <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
             <param name="own_file" value="bowtie2-ref.fasta" />
-            <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fastqsanger.gz paired-end datasets -->
@@ -737,7 +737,7 @@
             <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
             <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
             <param name="own_file" value="bowtie2-ref.fasta" />
-            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fastqsanger.bz2 paired-end datasets -->
@@ -749,7 +749,7 @@
             <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
             <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
             <param name="own_file" value="bowtie2-ref.fasta" />
-            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fasta paired-end datasets -->
@@ -761,7 +761,7 @@
             <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
             <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
             <param name="own_file" value="bowtie2-ref.fasta" />
-            <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="2"/>
+            <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4"/>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fasta paired-end datasets with bam_native as output -->