| Previous changeset 16:2dce91e11ca7 (2024-08-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c |
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modified:
macros.xml samtools_view.xml test-data/test_1.bam test-data/test_11.sam test-data/test_12.sam test-data/test_15.cram test-data/test_17.bam test-data/test_19.bam test-data/test_2.bam test-data/test_20.bam test-data/test_21.sam test-data/test_22.sam test-data/test_23.sam test-data/test_24.bam test-data/test_25.sam test-data/test_26.bam test-data/test_27.bam test-data/test_28.bam test-data/test_29.bam test-data/test_3.bam test-data/test_30.bam test-data/test_31.bam test-data/test_32.bam test-data/test_33.bam test-data/test_4.bam test-data/test_5.bam test-data/test_7.bam test-data/test_8.bam |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 macros.xml --- a/macros.xml Fri Aug 30 10:24:46 2024 +0000 +++ b/macros.xml Sun Sep 08 03:27:39 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 2dce91e11ca7 -r 32dc5f781059 samtools_view.xml --- a/samtools_view.xml Fri Aug 30 10:24:46 2024 +0000 +++ b/samtools_view.xml Sun Sep 08 03:27:39 2024 +0000 |
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| @@ -312,9 +312,7 @@ <param name="expression" type="text" argument="-e" label="Filter by expression - for example sclen>0 will filter all soft clipped reads" help="See Samtools manual for Filter expression syntax"> <sanitizer invalid_char=""> <valid initial="string.printable"> - <remove value=" "/> <remove value="'"/> - <remove value='"'/> </valid> </sanitizer> </param> |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_1.bam |
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| Binary file test-data/test_1.bam has changed |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_11.sam --- a/test-data/test_11.sam Fri Aug 30 10:24:46 2024 +0000 +++ b/test-data/test_11.sam Sun Sep 08 03:27:39 2024 +0000 |
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| @@ -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:1.15.1 CL:samtools view -@ 0 -h -o outfile infile +@PG ID:samtools PN:samtools PP:1 VN:1.20 CL:samtools view -@ 0 -h -o outfile infile 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 |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_12.sam --- a/test-data/test_12.sam Fri Aug 30 10:24:46 2024 +0000 +++ b/test-data/test_12.sam Sun Sep 08 03:27:39 2024 +0000 |
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| @@ -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:1.15.1 CL:samtools view -H -o outfile infile +@PG ID:samtools PN:samtools PP:1 VN:1.20 CL:samtools view -H -o outfile infile |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_15.cram |
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| Binary file test-data/test_15.cram has changed |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_17.bam |
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| Binary file test-data/test_17.bam has changed |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_19.bam |
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| Binary file test-data/test_19.bam has changed |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_2.bam |
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| Binary file test-data/test_2.bam has changed |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_20.bam |
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| Binary file test-data/test_20.bam has changed |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_21.sam --- a/test-data/test_21.sam Fri Aug 30 10:24:46 2024 +0000 +++ b/test-data/test_21.sam Sun Sep 08 03:27:39 2024 +0000 |
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| @@ -3,6 +3,7 @@ @RG ID:UNKNOWN SM:UNKNOWN @PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5 @PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2 -@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 24733 --subsample 0.20000000 -o outfile infile +@PG ID:samtools PN:samtools PP:0 VN:1.20 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 19923 --subsample 0.20000000 -o outfile infile +SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU +SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA <?@<@A8>0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU SRR065390.3743423 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ##################?6@:7<=@3=@ABAAB>BDBBABADABDDDBDDBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU -SRR065390.5238868 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA @,=@@D8D;?BBB>;?BBB==BB@D;>D>BBB>BBDDB<DABADCACDCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_22.sam --- a/test-data/test_22.sam Fri Aug 30 10:24:46 2024 +0000 +++ b/test-data/test_22.sam Sun Sep 08 03:27:39 2024 +0000 |
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| @@ -3,7 +3,7 @@ @RG ID:UNKNOWN SM:UNKNOWN @PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5 @PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2 -@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 5206 --subsample 1.00000000 -o outfile infile +@PG ID:samtools PN:samtools PP:0 VN:1.20 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 23928 --subsample 1.00000000 -o outfile infile SRR065390.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:1 XM:i:5 XN:i:0 XO:i:1 AS:i:-18 XS:i:-18 YT:Z:UU SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA <?@<@A8>0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_23.sam --- a/test-data/test_23.sam Fri Aug 30 10:24:46 2024 +0000 +++ b/test-data/test_23.sam Sun Sep 08 03:27:39 2024 +0000 |
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| @@ -4,4 +4,4 @@ @PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5 @PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2 @PG ID:samtools PN:samtools PP:0 VN:1.12 CL:samtools view -@ 0 -h -s .0 -o outfile infile -@PG ID:samtools.1 PN:samtools PP:samtools VN:1.15.1 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 23916 --subsample 1.00000000 -o outfile infile +@PG ID:samtools.1 PN:samtools PP:samtools VN:1.20 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 22460 --subsample 1.00000000 -o outfile infile |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_24.bam |
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| Binary file test-data/test_24.bam has changed |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_25.sam --- a/test-data/test_25.sam Fri Aug 30 10:24:46 2024 +0000 +++ b/test-data/test_25.sam Sun Sep 08 03:27:39 2024 +0000 |
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| @@ -3,7 +3,7 @@ @RG ID:UNKNOWN SM:UNKNOWN @PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5 @PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2 -@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 7 --subsample 0.20000000 -o outfile infile +@PG ID:samtools PN:samtools PP:0 VN:1.20 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 7 --subsample 0.20000000 -o outfile infile SRR065390.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:1 XM:i:5 XN:i:0 XO:i:1 AS:i:-18 XS:i:-18 YT:Z:UU SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU SRR065390.6023338 0 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAGCTAC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCDDDBCCABB=DABBA?################ RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-6 YT:Z:UU |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_26.bam |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_27.bam |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_7.bam |
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| diff -r 2dce91e11ca7 -r 32dc5f781059 test-data/test_8.bam --- a/test-data/test_8.bam Fri Aug 30 10:24:46 2024 +0000 +++ b/test-data/test_8.bam Sun Sep 08 03:27:39 2024 +0000 |
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| @@ -167,7 +167,7 @@ @SQ SN:GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT LN:0 @SQ SN:GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT LN:0 @SQ SN:TTCTTCCCCC LN:0 -@PG ID:samtools PN:samtools VN:1.15.1 CL:samtools view -@ 0 -h -o outfile infile +@PG ID:samtools PN:samtools VN:1.20 CL:samtools view -@ 0 -h -o outfile infile HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 |