# HG changeset patch
# User devteam
# Date 1450485679 18000
# Node ID 7fb926851f66f7086a5ce6e9204a5b9963eacec7
# Parent 317726be07032142cdb801dac0b8abe95a1e6f0a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
diff -r 317726be0703 -r 7fb926851f66 kraken-filter.xml
--- a/kraken-filter.xml Wed Jul 15 15:22:22 2015 -0400
+++ b/kraken-filter.xml Fri Dec 18 19:41:19 2015 -0500
@@ -5,6 +5,9 @@
macros.xml
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diff -r 317726be0703 -r 7fb926851f66 test-data/kraken_filter_test1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_filter_test1.tab Fri Dec 18 19:41:19 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 317726be0703 -r 7fb926851f66 test-data/kraken_filter_test1_output.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_filter_test1_output.tab Fri Dec 18 19:41:19 2015 -0500
@@ -0,0 +1,4 @@
+C gi|145231|gb|M33724.1|ECOALPHOA 83333 171 P=1.000 83333:162
+C gi|145232|gb|M33725.1|ECOALPHOB 83333 183 P=1.000 83333:174
+C gi|145234|gb|M33727.1|ECOALPHOE 83333 97 P=1.000 83333:88
+C gi|146195|gb|J01619.1|ECOGLTA 83333 3850 P=1.000 83333:3841
diff -r 317726be0703 -r 7fb926851f66 test-data/kraken_test1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_test1.fa Fri Dec 18 19:41:19 2015 -0500
@@ -0,0 +1,70 @@
+>gi|145231|gb|M33724.1|ECOALPHOA Escherichia coli K-12 truncated PhoA (phoA) gene, partial cds; and transposon Mu dI, partial sequence
+CAAAGCTCCGGGCCTCACCCAGGCGCTAAATACCAAAGATGGCGCAGTGATGGTGATGAGTTACGGGAAC
+TCCGAAGAGGATTCACAAGAACATACCGGCAGTCAGTTGCGTATTGCGGCGTATGGCCCGCATGCCGCCA
+ATGAAGCGGCGCACGAAAAACGCGAAAGCGT
+
+>gi|145232|gb|M33725.1|ECOALPHOB Escherichia coli K12 phoA pseudogene and transposon Mu dl-R, partial sequence
+CTGTCATAAAGTTGTCACGGCCGAGACTTATAGTCGCTTTGTTTTTATTTTTTAATGTATTTGTACATGG
+AGAAAATAAAGTGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTTTACCCCTGTGACAAAA
+GCCCGGACACCAGTGAAGCGGCGCACGAAAAACGCGAAAGCGT
+
+>gi|145234|gb|M33727.1|ECOALPHOE Escherichia coli K12 upstream sequence of psiA5::Mu dI. is identical to psiA30 upstream sequence; putative (phoA) pseudogene and transposon Mu dl-R, partial sequence
+TTGTTTTTATTTTTTAATGTATTTGTACATGGAGAAAATAAAGTGAAACAAAGCACTATTGCACTGGTGA
+AGCGGCGCACGAAAAACGCGAAAGCGT
+
+>gi|146195|gb|J01619.1|ECOGLTA Eschericia coli gltA gene, sdhCDAB operon and sucABCD operons, complete sequence
+GAATTCGACCGCCATTGCGCAAGGCATCGCCATGACCAGGCAGGATACAAAAGAGAGTCGATAAATATTC
+ACGGTGTCCATACCTGATAAATATTTTATGAAAGGCGGCGATGATGCCGCAAAATAATACTTATTTATAA
+TCCAGCACGTAGGTTGCGTTAGCGGTTACTTCACCTGCCGTGACATCGACTGCATTATCAATTTGTTCCA
+TCCAGGCGAAAAAGTTCAGCGTCTGTTCTGATGAGCTTGCATCCAGGTCAAGATCTGGCGCGGCTGAACC
+TAATACGATGTTACCGTCATTTTTGTCCATCAGTCGTACACCGACCCCAGTTGCTTCGCCTGCACTGGTG
+TTGCTCAACAAAGGCGTAGCACCAGTTGTCTTAGCCGTGCTATCGAAGGTTACGCCAAACTTTGGATACC
+GGCATTCCGCTACCGTTGTCAGAAGCAGGCAGATCACAGTTGATCAAGCGAATGTCGACGGCCACTTTAT
+TGCTATGATGCTCCCGGTTTATATGGGTTGTCGTGACTTGTCCAAGATCTATGTTTTTATCAATATCTTC
+TGGATGAATTTCACAAGGTGCTTCAATAACCTCCCCCTTAAAGTGAATTTCGCCAGAACCTTCATCAGCA
+GCATAAACAGGTGCAGTGAACAGCAGAGATACGGCCAGTGCGGCCAATGTTTTTTGTCCTTTAAACATAA
+CAGAGTCCTTTAAGGATATAGAATAGGGGTATAGCTACGCCAGAATATCGTATTTGATTATTGCTAGTTT
+TTAGTTTTGCTTAAAAAATATTGTTAGTTTTATTAAATTGGAAAACTAAATTATTGGTATCATGAATTGT
+TGTATGATGATAAATATAGGGGGGATATGATAGACGTCATTTTCATAGGGTTATAAAATGCGACTACCAT
+GAAGTTTTTAATTCAAAGTATTGGGTTGCTGATAATTTGAGCTGTTCTATTCTTTTTAAATATCTATATA
+GGTCTGTTAATGGATTTTATTTTTACAAGTTTTTTGTGTTTAGGCATATAAAAATCAAGCCCGCCATATG
+AACGGCGGGTTAAAATATTTACAACTTAGCAATCGAACCATTAACGCTTGATATCGCTTTTAAAGTCGCG
+TTTTTCATATCCTGTATACAGCTGACGCGGACGGGCAATCTTCATACCGTCACTGTGCATTTCGCTCCAG
+TGGGCGATCCAGCCAACGGTACGTGCCATTGCGAAAATGACGGTGAACATGGAAGACGGAATACCCATCG
+CTTTCAGGATGATACCAGAGTAGAAATCGACGTTCGGGTACAGTTTCTTCTCGATAAAGTACGGGTCGTT
+CAGCGCGATGTTTTCCAGCTCCATAGCCACTTCCAGCAGGTCATCCTTCGTGCCCAGCTCTTTCAGCACT
+TCATGGCAGGTTTCACGCATTACGGTGGCGCGCGGGTCGTAATTTTTGTACACGCGGTGACCGAAGCCCA
+TCAGGCGGAAAGAATCATTTTTGTCTTTCGCACGACGAAAAAATTCCGGAATGTGTTTAACGGAGCTGAT
+TTCTTCCAGCATTTTCAGCGCCGCTTCGTTAGCACCGCCGTGCGCAGGTCCCCACAGTGAAGCAATACCT
+GCTGCGATACAGGCAAACGGGTTCGCACCCGAAGAGCCAGCGGTACGCACGGTGGAGGTAGAGGCGTTCT
+GTTCATGGTCAGCGTGCAGGATCAGAATACGGTCCATAGCACGTTCCAGAATCGGATTAACTTCATACGG
+TTCGCACGGCGTGGAGAACATCATATTCAGGAAGTTACCGGCGTAGGAGAGATCGTTGCGCGGGTAAACA
+AATGGCTGACCAATGGAATACTTGTAACACATCGCGGCCATGGTCGGCATTTTCGACAGCAGGCGGAACG
+CGGCAATTTCACGGTGACGAGGATTGTTAACATCCAGCGAGTCGTGATAGAACGCCGCCAGCGCGCCGGT
+AATACCACACATGACTGCCATTGGATGCGAGTCGCGACGGAAAGCATGGAACAGACGGGTAATCTGCTCG
+TGGATCATGGTATGACGGGTCACCGTAGTTTTAAATTCGTCATACTGTTCCTGAGTCGGTTTTTCACCAT
+TCAGCAGGATGTAACAAACTTCCAGGTAGTTAGAATCGGTCGCCAGCTGATCGATCGGGAAACCGCGGTG
+CAGCAAAATACCTTCATCACCATCAATAAAAGTAATTTTAGATTCGCAGGATGCGGTTGAAGTGAAGCCT
+GGGTCAAAGGTGAACACACCTTTTGAACCGAGAGTACGGATATCAATAACATCTTGACCCAGCGTGCCTT
+TCAGCACATCCAGTTCAACAGCTGTATCCCCGTTGAGGGTGAGTTTTGCTTTTGTATCAGCCATTTAAGG
+TCTCCTTAGCGCCTTATTGCGTAAGACTGCCGGAACTTAAATTTGCCTTCGCACATCAACCTGGCTTTAC
+CCGTTTTTTATTTGGCTCGCCGCTCTGTGAAAGAGGGGAAAACCTGGGTACAGAGCTCTGGGCGCTTGCA
+GGTAAAGGATCCATTGATGACGAATAAATGGCGAATCAAGTACTTAGCAATCCGAATTATTAAACTTGTC
+TACCACTAATAACTGTCCCGAATGAATTGGTCAATACTCCACACTGTTACATAAGTTAATCTTAGGTGAA
+ATACCGACTTCATAACTTTTACGCATTATATGCTTTTCCTGGTAATGTTTGTAACAACTTTGTTGAATGA
+TTGTCAAATTAGATGATTAAAAATTAAATAAATGTTGTTATCGTGACCTGGATCACTGTTCAGGATAAAA
+CCCGACAAACTATATGTAGGTTAATTGTAATGATTTTGTGAACAGCCTATACTGCCGCCAGTCTCCGGAA
+CACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTGTCGTTTTCGCATCTGGAAGCAGTGTTTTGCATG
+ACGCGCAGTTATAGAAAGGACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAATCCCGACGTCTCCA
+GGTAACAGAAAGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGAACAGCATGTGGGCGTTATTC
+ATGATAAGAAATGTGAAAAAACAAAGACCTGTTAATCTGGACCTACAGACCATCCGGTTCCCCATCACGG
+CGATAGCGTCCATTCTCCATCGCGTTTCCGGTGTGATCACCTTTGTTGCAGTGGGCATCCTGCTGTGGCT
+TCTGGGTACCAGCCTCTCTTCCCCTGAAGGTTTCGAGCAAGCTTCCGCGATTATGGGCAGCTTCTTCGTC
+AAATTTATCATGTGGGGCATCCTTACCGCTCTGGCGTATCACGTCGTCGTAGGTATTCGCCACATGATGA
+TGGATTTTGGCTATCTGGAAGAAACATTCGAAGCGGGTAAACGCTCCGCCAAAATCTCCTTTGTTATTAC
+TGTCGTGCTTTCACTTCTCGCAGGAGTCCTCGTATGGTAAGCAACGCCTCCGCATTAGGACGCAATGGCG
+TACATGATTTCATCCTCGTTCGCGCTACCGCTATCGTCCTGACGCTCTACATCATTTATATGGTCGGTTT
+TTTCGCTACCAGTGGCGAGCTGACATATGAAGTCTGGATCGGTTTCTTCGCCTCTGCGTTCACCAAAGTG
+TTCACCCTGCTGGCGCTGTTTTCTATCTTGATCCATGCCTGGATCGGCATGTGGCAGGTGTTGACCGACT
+ACGTTAAACCGCTGGCTTTGCGCCTGATGCTGCAACTGGTGATTGTCGTTGCACTGGTGGTTTACGTGAT
+TTATGGATTCGTTGTGGTGTGGGGTGTGTGATGAAATTGCCAGTCAGAGAATTTGATGCAGTTGTGATTG
diff -r 317726be0703 -r 7fb926851f66 test-data/test_database.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database.loc Fri Dec 18 19:41:19 2015 -0500
@@ -0,0 +1,1 @@
+test_db test_db ${__HERE__}
\ No newline at end of file
diff -r 317726be0703 -r 7fb926851f66 test-data/test_db/database.idx
Binary file test-data/test_db/database.idx has changed
diff -r 317726be0703 -r 7fb926851f66 test-data/test_db/database.kdb
Binary file test-data/test_db/database.kdb has changed
diff -r 317726be0703 -r 7fb926851f66 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 19:41:19 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 317726be0703 -r 7fb926851f66 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 19:41:19 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 317726be0703 -r 7fb926851f66 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 19:41:19 2015 -0500
@@ -0,0 +1,8 @@
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