# HG changeset patch
# User devteam
# Date 1450485695 18000
# Node ID 9709eedcff4bde5442afa7445302ae922c1d19d1
# Parent a539aeea69fc81728d7680bd573331c1c459cb24
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
diff -r a539aeea69fc -r 9709eedcff4b kraken-mpa-report.xml
--- a/kraken-mpa-report.xml Wed Aug 05 12:13:09 2015 -0400
+++ b/kraken-mpa-report.xml Fri Dec 18 19:41:35 2015 -0500
@@ -35,6 +35,15 @@
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view a sample report of your classification
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macros.xml
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diff -r a539aeea69fc -r 9709eedcff4b 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 Fri Dec 18 19:41:35 2015 -0500
@@ -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 a539aeea69fc -r 9709eedcff4b 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 Fri Dec 18 19:41:35 2015 -0500
@@ -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 a539aeea69fc -r 9709eedcff4b 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 Fri Dec 18 19:41:35 2015 -0500
@@ -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 a539aeea69fc -r 9709eedcff4b test-data/kraken_report_test1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_report_test1.tab Fri Dec 18 19:41:35 2015 -0500
@@ -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 a539aeea69fc -r 9709eedcff4b 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 Fri Dec 18 19:41:35 2015 -0500
@@ -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 a539aeea69fc -r 9709eedcff4b test-data/test_database.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database.loc Fri Dec 18 19:41:35 2015 -0500
@@ -0,0 +1,1 @@
+test_db test_db ${__HERE__}
\ No newline at end of file
diff -r a539aeea69fc -r 9709eedcff4b test-data/test_db/database.idx
Binary file test-data/test_db/database.idx has changed
diff -r a539aeea69fc -r 9709eedcff4b test-data/test_db/database.kdb
Binary file test-data/test_db/database.kdb has changed
diff -r a539aeea69fc -r 9709eedcff4b 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 Fri Dec 18 19:41:35 2015 -0500
@@ -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 a539aeea69fc -r 9709eedcff4b 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 Fri Dec 18 19:41:35 2015 -0500
@@ -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 a539aeea69fc -r 9709eedcff4b tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Dec 18 19:41:35 2015 -0500
@@ -0,0 +1,8 @@
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