# HG changeset patch
# User iuc
# Date 1643617903 0
# Node ID cd659e8cc5fa5291e2bc45f74980f3f4a36bc764
# Parent  a6d65b0c67aff75f0795ead658951074760d0ac6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 37384c4ef9fee552914e0e13897ae4c37ef2d24a"

diff -r a6d65b0c67af -r cd659e8cc5fa bowtie2_macros.xml
--- a/bowtie2_macros.xml	Sat Jul 10 07:45:14 2021 +0000
+++ b/bowtie2_macros.xml	Mon Jan 31 08:31:43 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 a6d65b0c67af -r cd659e8cc5fa bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Sat Jul 10 07:45:14 2021 +0000
+++ b/bowtie2_wrapper.xml	Mon Jan 31 08:31:43 2022 +0000
@@ -1,11 +1,14 @@
 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05">
     <description>- map reads against reference genome</description>
+    <xrefs>
+        <xref type="bio.tools">bowtie2</xref>
+    </xrefs>
     <macros>
         <import>bowtie2_macros.xml</import>
     </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[
@@ -659,7 +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 -->
@@ -675,7 +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 -->
@@ -690,7 +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 -->
@@ -703,7 +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" />
@@ -722,7 +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 -->
@@ -734,7 +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 -->
@@ -746,7 +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 -->
@@ -758,7 +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 -->