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changeset 17:32dc5f781059 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:27:39 +0000
parents 2dce91e11ca7
children 48bbbcb692ce
files 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
diffstat 28 files changed, 11 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Fri Aug 30 10:24:46 2024 +0000
+++ b/macros.xml	Sun Sep 08 03:27:39 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
--- a/samtools_view.xml	Fri Aug 30 10:24:46 2024 +0000
+++ b/samtools_view.xml	Sun Sep 08 03:27:39 2024 +0000
@@ -312,9 +312,7 @@
                             <param name="expression" type="text" argument="-e" label="Filter by expression - for example sclen&gt;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>
Binary file test-data/test_1.bam has changed
--- 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
@@ -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
--- 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
@@ -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
Binary file test-data/test_15.cram has changed
Binary file test-data/test_17.bam has changed
Binary file test-data/test_19.bam has changed
Binary file test-data/test_2.bam has changed
Binary file test-data/test_20.bam has changed
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
Binary file test-data/test_24.bam has changed
--- 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
@@ -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
Binary file test-data/test_26.bam has changed
Binary file test-data/test_27.bam has changed
Binary file test-data/test_28.bam has changed
Binary file test-data/test_29.bam has changed
Binary file test-data/test_3.bam has changed
Binary file test-data/test_30.bam has changed
Binary file test-data/test_31.bam has changed
Binary file test-data/test_32.bam has changed
Binary file test-data/test_33.bam has changed
Binary file test-data/test_4.bam has changed
Binary file test-data/test_5.bam has changed
Binary file test-data/test_7.bam has changed
--- 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
@@ -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