| Previous changeset 1:773615269d71 (2023-02-13) Next changeset 3:88d274322340 (2023-03-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit afc6220b1e5f402f872338bbab440e4a1fe04ccd |
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modified:
kreport2krona.xml |
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added:
test-data/mpa_output.tabular test-data/mpa_output_intermediate.tabular test-data/mpa_output_percentages.tabular |
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| diff -r 773615269d71 -r d80c0fc14504 kreport2krona.xml --- a/kreport2krona.xml Mon Feb 13 10:23:39 2023 +0000 +++ b/kreport2krona.xml Mon Mar 06 21:22:47 2023 +0000 |
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| @@ -41,22 +41,27 @@ ------ A krona-compatible TEXT file -Example output: - --no-intermediate-ranks - 6298 Unclassified - 8 k__Bacteria - 4 k__Bacteria p_Proteobacteria - 6 k__Bacteria p_Proteobacteria c__Gammaproteobacteria - ... +**Example output:** + +``--no-intermediate-ranks`` + +:: + + 6298 Unclassified + 8 k__Bacteria + 4 k__Bacteria p_Proteobacteria + 6 k__Bacteria p_Proteobacteria c__Gammaproteobacteria - --intermediate-ranks - 6298 Unclassified - 79 x__root - 0 x__root x__cellular_organisms - 8 x__root x__cellular organisms k__Bacteria - 4 x__root x__cellular organisms k__Bacteria p__Proteobacteria - 6 x__root x__cellular organisms k__Bacteria p__Proteobacteria c__Gammaproteobacteria - .... +``--intermediate-ranks`` + +:: + + 6298 Unclassified + 79 x__root + 0 x__root x__cellular_organisms + 8 x__root x__cellular organisms k__Bacteria + 4 x__root x__cellular organisms k__Bacteria p__Proteobacteria + 6 x__root x__cellular organisms k__Bacteria p__Proteobacteria c__Gammaproteobacteria ]]></help> <expand macro="citations"/> |
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| diff -r 773615269d71 -r d80c0fc14504 test-data/mpa_output.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpa_output.tabular Mon Mar 06 21:22:47 2023 +0000 |
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| b'@@ -0,0 +1,215 @@\n+k__Eukaryota\t756\n+k__Eukaryota|k__Metazoa\t402\n+k__Eukaryota|k__Metazoa|p__Chordata\t402\n+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia\t402\n+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates\t402\n+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae\t402\n+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|g__Homo\t402\n+k__Eukaryota|k__Metazoa|p__Chordata|c__Mammalia|o__Primates|f__Hominidae|g__Homo|s__Homo_sapiens\t402\n+k__Eukaryota|k__Fungi\t342\n+k__Eukaryota|k__Fungi|p__Ascomycota\t341\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes\t336\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales\t336\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae\t333\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces\t329\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces_cerevisiae\t293\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces_paradoxus\t15\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Saccharomyces|s__Saccharomyces_eubayanus\t10\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Saccharomycetaceae|g__Kluyveromyces|s__Kluyveromyces_marxianus\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Trichomonascaceae\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Trichomonascaceae|g__Sugiyamaella\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Trichomonascaceae|g__Sugiyamaella|s__Sugiyamaella_lignohabitans\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Debaryomycetaceae\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Debaryomycetaceae|g__Candida\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Saccharomycetes|o__Saccharomycetales|f__Debaryomycetaceae|g__Candida|s__Candida_dubliniensis\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes\t3\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Sordariales|f__Sordariaceae|g__Neurospora|s__Neurospora_crassa\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Pyriculariaceae\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Pyriculariaceae|g__Pyricularia\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Sordariomycetes|o__Magnaporthales|f__Pyriculariaceae|g__Pyricularia|s__Pyricularia_pennisetigena\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Eurotiomycetes|o__Eurotiales|f__Aspergillaceae|g__Aspergillus|s__Aspergillus_luchuensis\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosaccharomycetales|f__Schizosaccharomycetaceae\t1\n+k__Eukaryota|k__Fungi|p__Ascomycota|c__Schizosaccharomycetes|o__Schizosac'..b'__Flavobacteriales\t3\n+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Blattabacteriaceae\t1\n+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Blattabacteriaceae|g__Blattabacterium\t1\n+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Blattabacteriaceae|g__Blattabacterium|s__Blattabacterium_cuenoti\t1\n+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae\t1\n+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Flavobacteriaceae|g__Olleya\t1\n+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae\t1\n+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium\t1\n+k__Bacteria|p__Bacteroidetes|c__Flavobacteriia|o__Flavobacteriales|f__Weeksellaceae|g__Chryseobacterium|s__Chryseobacterium_sp._DH-B6\t1\n+k__Bacteria|p__Bactero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| diff -r 773615269d71 -r d80c0fc14504 test-data/mpa_output_intermediate.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpa_output_intermediate.tabular Mon Mar 06 21:22:47 2023 +0000 |
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| b'@@ -0,0 +1,298 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|
| b |
| diff -r 773615269d71 -r d80c0fc14504 test-data/mpa_output_percentages.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mpa_output_percentages.tabular Mon Mar 06 21:22:47 2023 +0000 |
| b |
| b'@@ -0,0 +1,215 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