# HG changeset patch
# User iuc
# Date 1657103092 0
# Node ID f66e4858ca26a138489728b396d0f5f69c8237b0
# Parent  2f3400246bfc69b5283bb90594ddfb452a22e2da
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03

diff -r 2f3400246bfc -r f66e4858ca26 bowtie2_wrapper.xml
--- a/bowtie2_wrapper.xml	Mon Jan 31 08:31:13 2022 +0000
+++ b/bowtie2_wrapper.xml	Wed Jul 06 10:24:52 2022 +0000
@@ -1,11 +1,11 @@
-<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05">
+<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy1" profile="20.05">
     <description>- map reads against reference genome</description>
+    <macros>
+        <import>bowtie2_macros.xml</import>
+    </macros>
     <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="1.14">samtools</requirement>
@@ -662,7 +662,9 @@
             <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="4"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <test expect_num_outputs="3">
             <!-- test on list paired collection -->
@@ -678,7 +680,9 @@
                 </collection>
             </param>
             <param name="own_file" value="bowtie2-ref.fasta" />
-            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <!-- test on paired-end datasets with read group info -->
@@ -693,7 +697,9 @@
             <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="4"/>
+            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4" sort="true">
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <test expect_num_outputs="2">
             <!-- test on paired-end datasets with stats output -->
@@ -706,7 +712,9 @@
             <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="4"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
             <output name="mapping_stats">
                 <assert_contents>
                     <has_text text="of these" />
@@ -725,7 +733,9 @@
             <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="4"/>
+            <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4" sort="true">
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fastqsanger.gz paired-end datasets -->
@@ -737,7 +747,9 @@
             <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="4"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fastqsanger.bz2 paired-end datasets -->
@@ -749,7 +761,9 @@
             <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="4"/>
+            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fasta paired-end datasets -->
@@ -761,7 +775,9 @@
             <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="4"/>
+            <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4" sort="true">
+                <metadata name="sort_order" value="coordinate"/>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fasta paired-end datasets with bam_native as output -->
@@ -775,7 +791,9 @@
             <param name="own_file" value="bowtie2-ref.fasta" />
             <param name="sam_options_selector" value="yes" />
             <param name="reorder" value="true" />
-            <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
+            <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" lines_diff="4">
+                <metadata name="sort_order" value="unsorted"/>
+            </output>
         </test>
         <test expect_num_outputs="1">
             <!-- test on fasta paired-end datasets with sam as output -->
@@ -790,6 +808,7 @@
             <param name="sam_options_selector" value="yes" />
             <param name="sam_options|sam_opt" value="true" />
             <output name="output" ftype="sam">
+                <metadata name="sort_order" value="unsorted"/>
                 <assert_contents>
                     <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
                 </assert_contents>