| Previous changeset 13:0dbf49c414ae (2021-12-19) Next changeset 15:6be888be75f9 (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_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e |
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modified:
macros.xml samtools_view.xml test-data/test_21.sam test-data/test_22.sam test-data/test_25.sam |
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| diff -r 0dbf49c414ae -r 5826298f6a73 macros.xml --- a/macros.xml Sun Dec 19 15:58:19 2021 +0000 +++ b/macros.xml Mon Aug 15 09:19:43 2022 +0000 |
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| @@ -5,7 +5,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">1.13</token> + <token name="@TOOL_VERSION@">1.15.1</token> <token name="@PROFILE@">20.05</token> <token name="@FLAGS@"><![CDATA[ #set $flags = 0 @@ -103,7 +103,7 @@ #end if ]]></token> - <xml name="optional_reference"> + <xml name="optional_reference" token_help="" token_argument=""> <conditional name="addref_cond"> <param name="addref_select" type="select" label="Use a reference sequence"> <help>@HELP@</help> |
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| diff -r 0dbf49c414ae -r 5826298f6a73 samtools_view.xml --- a/samtools_view.xml Sun Dec 19 15:58:19 2021 +0000 +++ b/samtools_view.xml Mon Aug 15 09:19:43 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> <macros> <import>macros.xml</import> @@ -154,11 +154,11 @@ ## not dealing with all of the reads in the indexed ## file. We have to do an extra pass over the input to ## count the reads to subsample. - sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` && + sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` && #else: ## We can get the count of reads to subsample using ## an inexpensive call to idxstats. - sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` && + sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` && #end if #end if #end if @@ -690,7 +690,7 @@ </conditional> <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" /> </test> - <!-- 21) sampling options--> + <!-- 21) sampling options target < total reads --> <test> <param name="input" value="in_test_15.sam" ftype="sam" /> <conditional name="mode"> @@ -707,9 +707,9 @@ </conditional> </conditional> </conditional> - <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="6" /> + <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" /> </test> - <!-- 22) --> + <!-- 22) target > total reads --> <test> <param name="input" value="in_test_15.sam" ftype="sam" /> <conditional name="mode"> @@ -786,7 +786,7 @@ </conditional> </conditional> </conditional> - <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="6" /> + <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" /> </test> <!-- 26) --> <test> |
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| diff -r 0dbf49c414ae -r 5826298f6a73 test-data/test_21.sam --- a/test-data/test_21.sam Sun Dec 19 15:58:19 2021 +0000 +++ b/test-data/test_21.sam Mon Aug 15 09:19:43 2022 +0000 |
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| @@ -3,6 +3,6 @@ @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 -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 +@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 1 -h -f 0 -F 0 -G 0 -s 5.20000000 -o outfile infile +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 +SRR065390.6905811 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #######################BB@>A<BC>@@BCCB@=BACBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC 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 0dbf49c414ae -r 5826298f6a73 test-data/test_22.sam --- a/test-data/test_22.sam Sun Dec 19 15:58:19 2021 +0000 +++ b/test-data/test_22.sam Mon Aug 15 09:19:43 2022 +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:1.12 CL:samtools view -@ 0 -h -s .0 -o outfile infile +@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 1 -h -f 0 -F 0 -G 0 -s 0.00000000 -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 0dbf49c414ae -r 5826298f6a73 test-data/test_25.sam --- a/test-data/test_25.sam Sun Dec 19 15:58:19 2021 +0000 +++ b/test-data/test_25.sam Mon Aug 15 09:19:43 2022 +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:1.12 CL:samtools view -@ 0 -h -s 7.2 -o outfile infile +@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 1 -h -f 0 -F 0 -G 0 -s 7.20000000 -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 |