# HG changeset patch # User devteam # Date 1458576359 14400 # Node ID c4fb5dc47fce95dce06dc88f7dc1ead33019ccf8 # Parent 688428f6800fc13f7aca64a7983c7b22768525c7 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 3abfc7eb2999fa588862b84c453012c811fa8350 diff -r 688428f6800f -r c4fb5dc47fce kraken-mpa-report.xml --- a/kraken-mpa-report.xml Wed Aug 05 12:09:35 2015 -0400 +++ b/kraken-mpa-report.xml Mon Mar 21 12:05:59 2016 -0400 @@ -1,5 +1,5 @@ - + view report of classification for multiple samples macros.xml @@ -35,6 +35,15 @@ + + + + + + + + + + view a sample report of your classification + macros.xml + + + + + + + + + + + - - - diff -r 688428f6800f -r c4fb5dc47fce macros.xml --- a/macros.xml Wed Aug 05 12:09:35 2015 -0400 +++ b/macros.xml Mon Mar 21 12:05:59 2016 -0400 @@ -2,7 +2,10 @@ - kraken + kraken + + + kraken diff -r 688428f6800f -r c4fb5dc47fce test-data/kraken_mpa_report_input1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_mpa_report_input1.tab Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff -r 688428f6800f -r c4fb5dc47fce test-data/kraken_mpa_report_input2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_mpa_report_input2.tab Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff -r 688428f6800f -r c4fb5dc47fce test-data/kraken_mpa_report_test1_output.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_mpa_report_test1_output.tab Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,8 @@ +#Sample ID sample_0 sample_1 +d__Bacteria 4 4 +d__Bacteria|p__Proteobacteria 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia 4 4 +d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli 4 4 diff -r 688428f6800f -r c4fb5dc47fce test-data/kraken_report_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_report_test1.tab Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,4 @@ +C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 83333:162 +C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 83333:174 +C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 83333:88 +C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 83333:3841 diff -r 688428f6800f -r c4fb5dc47fce test-data/kraken_report_test1_output.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_report_test1_output.tab Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,11 @@ + 0.00 0 0 U 0 unclassified +100.00 4 0 - 1 root +100.00 4 0 - 131567 cellular organisms +100.00 4 0 D 2 Bacteria +100.00 4 0 P 1224 Proteobacteria +100.00 4 0 C 1236 Gammaproteobacteria +100.00 4 0 O 91347 Enterobacteriales +100.00 4 0 F 543 Enterobacteriaceae +100.00 4 0 G 561 Escherichia +100.00 4 0 S 562 Escherichia coli +100.00 4 4 - 83333 Escherichia coli K-12 diff -r 688428f6800f -r c4fb5dc47fce test-data/test_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_database.loc Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,1 @@ +test_db test_db ${__HERE__} \ No newline at end of file diff -r 688428f6800f -r c4fb5dc47fce test-data/test_db/database.idx Binary file test-data/test_db/database.idx has changed diff -r 688428f6800f -r c4fb5dc47fce test-data/test_db/database.kdb Binary file test-data/test_db/database.kdb has changed diff -r 688428f6800f -r c4fb5dc47fce test-data/test_db/taxonomy/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/taxonomy/names.dmp Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,74 @@ +83333 | Escherichia coli K-12 | | scientific name | +83333 | Escherichia coli K12 | | equivalent name | +562 | "Bacillus coli" Migula 1895 | | authority | +562 | "Bacterium coli commune" Escherich 1885 | | authority | +562 | "Bacterium coli" (Migula 1895) Lehmann and Neumann 1896 | | authority | +562 | ATCC 11775 | | type material | +562 | Bacillus coli | | synonym | +562 | Bacterium coli | | synonym | +562 | Bacterium coli commune | | synonym | +562 | CCUG 24 | | type material | +562 | CCUG 29300 | | type material | +562 | CIP 54.8 | | type material | +562 | DSM 30083 | | type material | +562 | Enterococcus coli | | synonym | +562 | Escherchia coli | | misspelling | +562 | Escherichia coli | | scientific name | +562 | Escherichia coli (Migula 1895) Castellani and Chalmers 1919 | | authority | +562 | Escherichia sp. MAR | | includes | +562 | Escherichia/Shigella coli | | equivalent name | +562 | Eschericia coli | | misspelling | +562 | JCM 1649 | | type material | +562 | LMG 2092 | | type material | +562 | NBRC 102203 | | type material | +562 | NCCB 54008 | | type material | +562 | NCTC 9001 | | type material | +562 | bacterium 10a | | includes | +562 | bacterium E3 | | includes | +561 | Escherchia | | misspelling | +561 | Escherichia | | scientific name | +561 | Escherichia Castellani and Chalmers 1919 | | authority | +543 | Enterobacteraceae | | synonym | +543 | Enterobacteraceae (ex Lapage 1979) Lapage 1982, fam. nov., nom. rev. | | synonym | +543 | Enterobacteriaceae | | scientific name | +543 | Enterobacteriaceae (ex Rahn 1937) Ewing et al. 1980, fam. nov., nom. rev. | | synonym | +543 | Enterobacteriaceae Rahn 1937 | | synonym | +543 | gamma-3 proteobacteria | gamma-3 proteobacteria <#1> | in-part | +91347 | 'Enterobacteriales' | | synonym | +91347 | Enterobacteriaceae and related endosymbionts | | synonym | +91347 | Enterobacteriaceae group | | synonym | +91347 | Enterobacteriales | | scientific name | +91347 | enterobacteria | enterobacteria | blast name | +91347 | gamma-3 proteobacteria | gamma-3 proteobacteria <#5> | in-part | +1236 | Gammaproteobacteria | | scientific name | +1236 | Gammaproteobacteria Garrity et al. 2005 | | synonym | +1236 | Proteobacteria gamma subdivision | | synonym | +1236 | Purple bacteria, gamma subdivision | | synonym | +1236 | g-proteobacteria | gamma proteos | blast name | +1236 | gamma proteobacteria | | synonym | +1236 | gamma subdivision | | synonym | +1236 | gamma subgroup | | synonym | +1224 | Proteobacteria | | scientific name | +1224 | Proteobacteria Garrity et al. 2005 | | authority | +1224 | Proteobacteria [class] Stackebrandt et al. 1988 | | authority | +1224 | not Proteobacteria Cavalier-Smith 2002 | | authority | +1224 | proteobacteria | proteobacteria | blast name | +1224 | purple bacteria | | common name | +1224 | purple bacteria and relatives | | common name | +1224 | purple non-sulfur bacteria | | common name | +1224 | purple photosynthetic bacteria | | common name | +1224 | purple photosynthetic bacteria and relatives | | common name | +2 | Bacteria | Bacteria | scientific name | +2 | Monera | Monera | in-part | +2 | Procaryotae | Procaryotae | in-part | +2 | Prokaryota | Prokaryota | in-part | +2 | Prokaryotae | Prokaryotae | in-part | +2 | bacteria | bacteria | blast name | +2 | eubacteria | | genbank common name | +2 | not Bacteria Haeckel 1894 | | synonym | +2 | prokaryote | prokaryote | in-part | +2 | prokaryotes | prokaryotes | in-part | +1 | all | | synonym | +1 | root | | scientific name | +131567 | biota | | synonym | +131567 | cellular organisms | | scientific name | diff -r 688428f6800f -r c4fb5dc47fce test-data/test_db/taxonomy/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_db/taxonomy/nodes.dmp Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,10 @@ +83333 | 562 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +562 | 561 | species | EC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +561 | 543 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +543 | 91347 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +91347 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | diff -r 688428f6800f -r c4fb5dc47fce tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Mar 21 12:05:59 2016 -0400 @@ -0,0 +1,8 @@ + + + + + value, name, path + +

+ diff -r 688428f6800f -r c4fb5dc47fce tool_dependencies.xml --- a/tool_dependencies.xml Wed Aug 05 12:09:35 2015 -0400 +++ b/tool_dependencies.xml Mon Mar 21 12:05:59 2016 -0400 @@ -1,6 +1,6 @@ - - + +