# HG changeset patch
# User iuc
# Date 1575397810 0
# Node ID 6e690205b306911d0e581ce967d2091994b3a10a
# Parent ccfb9cbfcc72526acaaabf42349f665f6fbc61f4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 1590e274eaa41ea77a6017111f9122e0a58aa75d-dirty"
diff -r ccfb9cbfcc72 -r 6e690205b306 kraken-filter.xml
--- a/kraken-filter.xml Mon Aug 07 17:27:49 2017 -0400
+++ b/kraken-filter.xml Tue Dec 03 18:30:10 2019 +0000
@@ -26,11 +26,11 @@
-
+
-
+
-
+
diff -r ccfb9cbfcc72 -r 6e690205b306 macros.xml
--- a/macros.xml Mon Aug 07 17:27:49 2017 -0400
+++ b/macros.xml Tue Dec 03 18:30:10 2019 +0000
@@ -1,9 +1,9 @@
- 1.2.3
+ 1.3.1
- kraken
+ kraken
@@ -23,6 +23,10 @@
10.1186/gb-2014-15-3-r46
- --db ${kraken_database.fields.name}
- export KRAKEN_DB_PATH="${kraken_database.fields.path}"
+
+ if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi
+ --db "\$KRAKEN_DEFAULT_DB"
diff -r ccfb9cbfcc72 -r 6e690205b306 test-data/kraken-filter/kraken_filter_test1.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken-filter/kraken_filter_test1.tab Tue Dec 03 18:30:10 2019 +0000
@@ -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 ccfb9cbfcc72 -r 6e690205b306 test-data/kraken-filter/kraken_filter_test1_output.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken-filter/kraken_filter_test1_output.tab Tue Dec 03 18:30:10 2019 +0000
@@ -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 ccfb9cbfcc72 -r 6e690205b306 test-data/kraken-filter/kraken_test1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken-filter/kraken_test1.fa Tue Dec 03 18:30:10 2019 +0000
@@ -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 ccfb9cbfcc72 -r 6e690205b306 test-data/kraken_filter_test1.tab
--- a/test-data/kraken_filter_test1.tab Mon Aug 07 17:27:49 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-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 ccfb9cbfcc72 -r 6e690205b306 test-data/kraken_filter_test1_output.tab
--- a/test-data/kraken_filter_test1_output.tab Mon Aug 07 17:27:49 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-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 ccfb9cbfcc72 -r 6e690205b306 test-data/kraken_test1.fa
--- a/test-data/kraken_test1.fa Mon Aug 07 17:27:49 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
->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 ccfb9cbfcc72 -r 6e690205b306 test-data/test_database.loc
--- a/test-data/test_database.loc Mon Aug 07 17:27:49 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-test_db test_db ${__HERE__}
\ No newline at end of file
diff -r ccfb9cbfcc72 -r 6e690205b306 test-data/test_db/database.idx
Binary file test-data/test_db/database.idx has changed
diff -r ccfb9cbfcc72 -r 6e690205b306 test-data/test_db/database.kdb
Binary file test-data/test_db/database.kdb has changed
diff -r ccfb9cbfcc72 -r 6e690205b306 test-data/test_db/taxonomy/names.dmp
--- a/test-data/test_db/taxonomy/names.dmp Mon Aug 07 17:27:49 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-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 ccfb9cbfcc72 -r 6e690205b306 test-data/test_db/taxonomy/nodes.dmp
--- a/test-data/test_db/taxonomy/nodes.dmp Mon Aug 07 17:27:49 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-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 ccfb9cbfcc72 -r 6e690205b306 tool-data/kraken_databases.loc.sample
--- a/tool-data/kraken_databases.loc.sample Mon Aug 07 17:27:49 2017 -0400
+++ b/tool-data/kraken_databases.loc.sample Tue Dec 03 18:30:10 2019 +0000
@@ -0,0 +1,18 @@
+# Expect three columns, tab separated, as follows:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (folder name containing the Kraken DB)
+#
+# e.g.
+# plants2018Plant genomes (2018)/path/to/krakenDB/plants_2018
+#
+# For backward compatibility the Kraken wrapper also accepts:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Final part of folder name, Galaxy shows this in the UI)
+# - path (Parent folder name, where $path/$name contains the Kraken DB)
+#
+# e.g.
+# plants2018plants_2018/path/to/krakenDB
+#
+# Please avoid this legacy usage, as not all tools using
+# the kraken_databases.loc file will understand it.