| Previous changeset 8:a389f74c3630 (2023-11-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c |
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modified:
macros.xml samtools_markdup.xml test-data/11_markdup.expected.cram test-data/1_markdup.expected.bam test-data/2_remove_dups.expected.bam test-data/3_mark_supp_dup.expected.bam test-data/6_markdup.expected.bam test-data/7_markdup.expected.bam test-data/8_markdup.expected.bam test-data/9_markdup.expected.sam test-data/stats.txt |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 --> |
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| diff -r a389f74c3630 -r 40fa6c240105 test-data/11_markdup.expected.cram |
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| Binary file test-data/11_markdup.expected.cram has changed |
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| diff -r a389f74c3630 -r 40fa6c240105 test-data/1_markdup.expected.bam |
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| Binary file test-data/1_markdup.expected.bam has changed |
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| diff -r a389f74c3630 -r 40fa6c240105 test-data/2_remove_dups.expected.bam |
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| Binary file test-data/2_remove_dups.expected.bam has changed |
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| diff -r a389f74c3630 -r 40fa6c240105 test-data/3_mark_supp_dup.expected.bam |
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| Binary file test-data/3_mark_supp_dup.expected.bam has changed |
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| diff -r a389f74c3630 -r 40fa6c240105 test-data/6_markdup.expected.bam |
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| Binary file test-data/6_markdup.expected.bam has changed |
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| diff -r a389f74c3630 -r 40fa6c240105 test-data/7_markdup.expected.bam |
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| Binary file test-data/7_markdup.expected.bam has changed |
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| diff -r a389f74c3630 -r 40fa6c240105 test-data/8_markdup.expected.bam |
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| Binary file test-data/8_markdup.expected.bam has changed |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 + |