# HG changeset patch
# User iuc
# Date 1725765974 0
# Node ID 40fa6c24010532a10591fcf794202127b760ea87
# Parent  a389f74c3630ea64f67efbf399bb8b4102145c8f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c

diff -r a389f74c3630 -r 40fa6c240105 macros.xml
--- a/macros.xml	Mon Nov 20 22:15:54 2023 +0000
+++ b/macros.xml	Sun Sep 08 03:26:14 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 a389f74c3630 -r 40fa6c240105 samtools_markdup.xml
--- a/samtools_markdup.xml	Mon Nov 20 22:15:54 2023 +0000
+++ b/samtools_markdup.xml	Sun Sep 08 03:26:14 2024 +0000
@@ -127,7 +127,8 @@
             <param name="bamfile" value="3_two_read_mapped.sam" ftype="sam" />
             <param name="stats" value="yes"/>
             <assert_stderr>
-                <has_line line="[markdup] error: no MC tag. Please run samtools fixmate on file first."/>
+                <has_line line="samtools markdup: error, no MC tag. Please run samtools fixmate on file first."/>
+                <has_line line="samtools markdup: error, unable to assign pair hash key."/>
             </assert_stderr>
         </test>
         <!-- 6) check optical distance and check -c option -->
diff -r a389f74c3630 -r 40fa6c240105 test-data/11_markdup.expected.cram
Binary file test-data/11_markdup.expected.cram has changed
diff -r a389f74c3630 -r 40fa6c240105 test-data/1_markdup.expected.bam
Binary file test-data/1_markdup.expected.bam has changed
diff -r a389f74c3630 -r 40fa6c240105 test-data/2_remove_dups.expected.bam
Binary file test-data/2_remove_dups.expected.bam has changed
diff -r a389f74c3630 -r 40fa6c240105 test-data/3_mark_supp_dup.expected.bam
Binary file test-data/3_mark_supp_dup.expected.bam has changed
diff -r a389f74c3630 -r 40fa6c240105 test-data/6_markdup.expected.bam
Binary file test-data/6_markdup.expected.bam has changed
diff -r a389f74c3630 -r 40fa6c240105 test-data/7_markdup.expected.bam
Binary file test-data/7_markdup.expected.bam has changed
diff -r a389f74c3630 -r 40fa6c240105 test-data/8_markdup.expected.bam
Binary file test-data/8_markdup.expected.bam has changed
diff -r a389f74c3630 -r 40fa6c240105 test-data/9_markdup.expected.sam
--- a/test-data/9_markdup.expected.sam	Mon Nov 20 22:15:54 2023 +0000
+++ b/test-data/9_markdup.expected.sam	Sun Sep 08 03:26:14 2024 +0000
@@ -1,7 +1,7 @@
 @HD	VN:1.4	SO:coordinate
 @SQ	SN:contig_000000000	LN:11391
-@PG	ID:samtools	PN:samtools	VN:1.12	CL:samtools sort -@ 0 -m 768M -T . -O sam -o coordsort.sam /tmp/tmpuzvw6tdp/files/b/a/d/dataset_badf390c-6dae-4603-937a-f000db10e1eb.dat
-@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.12	CL:samtools markdup -@ 0 -m t -O SAM coordsort.sam /tmp/tmpuzvw6tdp/files/c/4/1/dataset_c4121439-d0e4-4e9a-b597-951d44bf57bc.dat
+@PG	ID:samtools	PN:samtools	VN:1.20	CL:samtools sort -@ 0 -m 768M -T /tmp/tmpo1hsz7dc/tmp -O sam -o coordsort.sam /tmp/tmpo1hsz7dc/files/1/a/f/dataset_1afa2f60-62b8-4548-bb89-e30d23322a3e.dat
+@PG	ID:samtools.1	PN:samtools	PP:samtools	VN:1.20	CL:samtools markdup -@ 0 -m t -O SAM coordsort.sam /tmp/tmpo1hsz7dc/job_working_directory/000/20/outputs/dataset_5a651845-a763-4ddc-ac05-3734afca2130.dat
 entry1	1187	contig_000000000	109	60	250M	=	137	278	GATTGATATTTATTTATTATTTTATTATGTTTATTTCTTTATTTATTATCATTATTATTATTATTCTTATTATTGTTATATAAAAACATCGTAAACACAGTAAACGATAGTACTAATACTACTACTAATAAAGATAGATTTTTTTATATATATATATGTATGATCTTTTAACGTTACTTATTCAAATGCTATGTCATTTTGTAATATTTGTCATGGCAAGTATCAAACTGCTTCGGTTCTCATTGATTAG	1111>DD3DFFF3B333B3FBG3D3A33BG3D3F3333AFG3DF3D33B22D22222222D2B2A2ADE2AA2DAG222BD22D11//11//00B110ABB2FD1?>/>A2@2@2@F2@F21GB11FDDF21111111B2B11>/?1FB22>>>22>B2BG22B12B>F>11/0<0/2B2222B2@G11>22@22@G222201?1??1<?DF1FG1001<1>1F1=11>111>1-....000=0000=00	NM:i:18	AS:i:164	XS:i:0	MQ:i:60	MC:Z:250M	ms:i:6744
 entry2	163	contig_000000000	109	60	250M	=	137	278	TATTGATATTTATTTATTATTTTATTATGTTTATTTATTTATTTATTATCATTATTATTATTATTATTATTATTGTTATATACAAACATAGTAAACACAGTAAACGATAGTAGTAATACTACTACTAATAAATATATATTTTTTTATATATATATATGTATGTTCTTTTAATGTTAATTTTTCAAATGCTTTGGCATTTTGTAACATTTGTCATGCCATGTATCAAACTGCCTGGGTTATCATTGATTAG	BBBBB5F5DFFFGGGFGGGGGGHHHHHHHHHGHHGHHHHHHHHHHHHGGHHHHHHHEHHGHHGHHFHHHHHGHHHHHFHHHD5A33FBGBFHGGGFGGEGGGBGGAEGAEHH5GD5FEGFD5GGFGHFHE4GHGGHHHHHHHDEEA?FGHHGHGHFBEFFHEGHH4GGHHCFFFHHFHHHHHHBFHG1FFBFF01BGHHHFCFF@1GHHBGGFHFF1?1?FBGGF11FD110FG.<FFGGH1FGH0DG00	NM:i:2	AS:i:240	XS:i:0	MQ:i:60	MC:Z:250M	ms:i:9279
 entry3	99	contig_000000000	116	60	250M	=	222	356	ATTTATTTATTATTTTATTATGTTTATTTATTTATTTATTATCATTATTATTATTATTATTATTATTGTTATATAAAAACATAGTAAACACAGTAAACGATAGTAGTAATACTACTACTAATAAATATATATTTTTTTATATATATATATGTATGTTCTTTTAATGTTAATTTTTCAAATGCTTTGGCATTTTGTAACATTTGTCATGCCAAGTATCAAACTGCCTGGGTTATCATTGATTAGGTACTAG	BBBBBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHGGHGGHGHHHHHGHHHHHHHHHFHHHGHHGHHHHGHHHGGHHHHHHHHHHHHHGHHHHHGHHHHIHHHIIHHHHHHHGHGHHHGHHHHGHHHGHHGHHHHGHHHHHHGHBFFHHHHHHHGHHHGHEHHHFFGGHHHHHHHEHHHFH=GHHHF	NM:i:0	AS:i:250	XS:i:0	MQ:i:60	MC:Z:250M	ms:i:9509
diff -r a389f74c3630 -r 40fa6c240105 test-data/stats.txt
--- a/test-data/stats.txt	Mon Nov 20 22:15:54 2023 +0000
+++ b/test-data/stats.txt	Sun Sep 08 03:26:14 2024 +0000
@@ -1,4 +1,4 @@
-COMMAND: samtools markdup -@ 0 -s coordsort.sam /tmp/tmpea8lprdd/files/2/2/4/dataset_224df993-f6bf-4c7d-99a1-2e9dd51c2a57.dat
+COMMAND: samtools markdup -@ 0 -m t -s -f /tmp/tmpo1hsz7dc/job_working_directory/000/8/outputs/dataset_9e69bd59-3165-4ede-92bf-2f438627a6a1.dat -O BAM coordsort.sam /tmp/tmpo1hsz7dc/job_working_directory/000/8/outputs/dataset_ccf59cfe-ffbd-41d5-9412-d7a7ac6e65d9.dat
 READ: 16
 WRITTEN: 16
 EXCLUDED: 3
@@ -14,3 +14,4 @@
 DUPLICATE PRIMARY TOTAL: 6
 DUPLICATE TOTAL: 6
 ESTIMATED_LIBRARY_SIZE: 4
+