# HG changeset patch
# User iuc
# Date 1725765895 0
# Node ID 3c661e57a88f49133c6461e66764d28ea1c8d735
# Parent  a53efedba9e767c3b58f7a3bc8cb1b74c3c7a8ea
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/bam_to_sam commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

diff -r a53efedba9e7 -r 3c661e57a88f macros.xml
--- a/macros.xml	Mon Nov 20 22:14:02 2023 +0000
+++ b/macros.xml	Sun Sep 08 03:24:55 2024 +0000
@@ -11,9 +11,9 @@
          please only bump the minor version in order to let the requirement
          version catch up eventually). To find the tools check:
         `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
-    <token name="@TOOL_VERSION@">1.15.1</token>
+    <token name="@TOOL_VERSION@">1.20</token>
     <token name="@VERSION_SUFFIX@">2</token>
-    <token name="@PROFILE@">20.05</token>
+    <token name="@PROFILE@">22.05</token>
     <token name="@FLAGS@"><![CDATA[
         #set $flags = 0
         #if $filter
diff -r a53efedba9e7 -r 3c661e57a88f test-data/bam_to_sam_out1.sam
--- a/test-data/bam_to_sam_out1.sam	Mon Nov 20 22:14:02 2023 +0000
+++ b/test-data/bam_to_sam_out1.sam	Sun Sep 08 03:24:55 2024 +0000
@@ -4,7 +4,7 @@
 @SQ	SN:chr8	LN:202
 @RG	ID:0	SM:Hi,Mom!
 @PG	ID:1	PN:Hey!	VN:2.0
-@PG	ID:samtools	PN:samtools	PP:1	VN:1.12	CL:samtools view -o /tmp/tmpl_eh5cxt/files/3/b/2/dataset_3b2eeebc-108d-4ce9-a5b9-17e224264121.dat -h /tmp/tmpl_eh5cxt/files/1/2/d/dataset_12de9904-ebd8-436b-a125-8f034068385e.dat
+@PG	ID:samtools	PN:samtools	PP:1	VN:1.20	CL:samtools view -o /tmp/tmp3bwmizj1/job_working_directory/000/2/outputs/dataset_f1239316-7904-41f9-b3dd-a740a70acf8b.dat -h /tmp/tmp3bwmizj1/files/4/4/a/dataset_44af64ee-5cc1-4454-9cf0-6a3a24296b69.dat
 both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
 both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
 read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
diff -r a53efedba9e7 -r 3c661e57a88f test-data/bam_to_sam_out2.sam
--- a/test-data/bam_to_sam_out2.sam	Mon Nov 20 22:14:02 2023 +0000
+++ b/test-data/bam_to_sam_out2.sam	Sun Sep 08 03:24:55 2024 +0000
@@ -4,4 +4,4 @@
 @SQ	SN:chr8	LN:202
 @RG	ID:0	SM:Hi,Mom!
 @PG	ID:1	PN:Hey!	VN:2.0
-@PG	ID:samtools	PN:samtools	PP:1	VN:1.12	CL:samtools view -o /tmp/tmpl_eh5cxt/files/3/0/2/dataset_3025757e-159d-4ced-a398-2d7dc823e34b.dat -H /tmp/tmpl_eh5cxt/files/9/5/d/dataset_95dbe51c-ade9-4f37-9399-79ec158c1516.dat
+@PG	ID:samtools	PN:samtools	PP:1	VN:1.20	CL:samtools view -o /tmp/tmp3bwmizj1/job_working_directory/000/4/outputs/dataset_e689a4f6-7c14-4a65-9155-214ed5cbcfa7.dat -H /tmp/tmp3bwmizj1/files/7/d/5/dataset_7d5cef18-567a-4e59-86c6-0dcadae11b36.dat