| Previous changeset 2:f03c7ba8d8bc (2017-04-26) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/ commit 45d0409859aca5b099dba7e0acd472f5703240e1 |
|
modified:
kraken2tax.xml test-data/kraken2tax-test1.txt test-data/kraken2tax.txt |
|
added:
test-data/ncbi_taxonomy.loc.test test-data/tax_dir/names.dmp test-data/tax_dir/nodes.dmp tool_data_table_conf.xml.test |
| b |
| diff -r f03c7ba8d8bc -r 50bd98b3ae5a kraken2tax.xml --- a/kraken2tax.xml Wed Apr 26 14:11:06 2017 -0400 +++ b/kraken2tax.xml Fri Sep 29 14:38:33 2023 +0000 |
| [ |
| @@ -1,8 +1,8 @@ -<tool id="Kraken2Tax" name="Convert Kraken" version="1.2"> +<tool id="Kraken2Tax" name="Convert Kraken" version="1.2+galaxy0"> <description>data to Galaxy taxonomy representation</description> <requirements> - <requirement type="package" version="4.1.0">gawk</requirement> - <requirement type="package" version="1.0.0">gb_taxonomy_tools</requirement> + <requirement type="package" version="5.1.0">gawk</requirement> + <requirement type="package" version="1.0.1">gb_taxonomy_tools</requirement> </requirements> <command> <![CDATA[ |
| b |
| diff -r f03c7ba8d8bc -r 50bd98b3ae5a test-data/kraken2tax-test1.txt --- a/test-data/kraken2tax-test1.txt Wed Apr 26 14:11:06 2017 -0400 +++ b/test-data/kraken2tax-test1.txt Fri Sep 29 14:38:33 2023 +0000 |
| b |
| b'@@ -1,3415 +1,1 @@\n-M02286:29:000000000-AA53D:1:1114:23595:17370\t48479\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1104:21103:22897\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1116:7859:10478\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1119:6631:17714\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:16922:6472\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:7160:7695\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:20532:9912\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:19340:10214\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1101:5996:10649\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:20475:11020\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:10048:11525\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1101:18885:13163\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:13519:14170\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:13574:14586\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:19460:16940\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1101:16657:19082\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:4041:20103\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:5627:22484\t34034\troot\tBacteria\tn\tn\tn\tProteobacteria\tdelta/epsilon subdivisions\tn\tDeltaproteobacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured delta proteobacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:9936:22774\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1102:25342:6405\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:20935:6873\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:6525:6886\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:25191:6951\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:6767:7217\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1102:19795:7861\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:6324:8095\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1102:12143:9421\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:16903:9943\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:6643:10300\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:4204:12843\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1102:8526:14536\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:14191:16205\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1102:8537:16586\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultu'..b':000000000-AA53D:1:2105:27848:11057\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:2109:14547:16056\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:2116:8415:20212\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:2111:13059:9985\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1101:11218:18482\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1108:23719:8436\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:2112:9415:20030\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:2105:24502:18789\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:2104:19106:20150\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:2110:6159:5038\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:2107:28345:16458\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:2105:15748:20757\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:2110:4035:5602\t152509\troot\tBacteria\tn\tn\tBacteroidetes/Chlorobi group\tBacteroidetes\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured Bacteroidetes bacterium\tn\t\n-M02286:29:000000000-AA53D:1:2112:10518:18769\t155900\troot\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured organism\tn\t\n-M02286:29:000000000-AA53D:1:2111:13968:11139\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:2111:24542:14435\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1119:23951:3621\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1108:12019:7678\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1103:15691:18080\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1114:15782:7171\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1116:26163:21828\t1654\troot\tBacteria\tn\tn\tn\tActinobacteria\tn\tn\tActinobacteria\tn\tn\tActinomycetales\tn\tn\tActinomycetaceae\tn\tn\tn\tActinomyces\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1101:16009:8262\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1104:4948:9359\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1104:7127:11365\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1108:7315:10840\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1108:22055:17293\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1117:8041:5693\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:1117:22456:10966\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1117:24299:12438\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1119:17233:7295\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1119:16223:13539\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n-M02286:29:000000000-AA53D:1:2101:15742:10457\t2\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n-M02286:29:000000000-AA53D:1:1104:13419:19934\t77133\troot\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tuncultured bacterium\tn\t\n+M02286:29:000000000-AA53D:1:1104:21103:22897\t2\tBacteria\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\tn\t\n' |
| b |
| diff -r f03c7ba8d8bc -r 50bd98b3ae5a test-data/kraken2tax.txt --- a/test-data/kraken2tax.txt Wed Apr 26 14:11:06 2017 -0400 +++ b/test-data/kraken2tax.txt Fri Sep 29 14:38:33 2023 +0000 |
| b |
| b'@@ -1,3415 +1,1 @@\n-C\tM02286:29:000000000-AA53D:1:1114:23595:17370\t48479\t477\tQ:1\n C\tM02286:29:000000000-AA53D:1:1104:21103:22897\t2\t466\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1116:7859:10478\t77133\t466\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1119:6631:17714\t77133\t466\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:16922:6472\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:7160:7695\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:20532:9912\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:19340:10214\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:5996:10649\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:20475:11020\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:10048:11525\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:18885:13163\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:13519:14170\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:13574:14586\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:19460:16940\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:16657:19082\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:4041:20103\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:5627:22484\t34034\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:9936:22774\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:25342:6405\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:20935:6873\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:6525:6886\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:25191:6951\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:6767:7217\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:19795:7861\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:6324:8095\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:12143:9421\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:16903:9943\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:6643:10300\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:4204:12843\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:8526:14536\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:14191:16205\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:8537:16586\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:19473:17553\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:19484:17570\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:23641:17757\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:19761:20542\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:19352:22325\t748449\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:18110:23346\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:7518:2823\t748449\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:7534:2833\t748449\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:6273:4020\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:6682:5153\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:4812:5234\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:5108:7364\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:16425:8610\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:26229:10822\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:6024:10960\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:13912:12336\t748449\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:9574:12899\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:9388:12947\t748449\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:24471:15101\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:19077:15101\t31989\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:11082:15358\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:18649:15600\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:25050:18100\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:16239:18331\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:15144:18604\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:20011:18964\t2\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:14085:19348\t48479\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:22338:19477\t748449\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:17127:6563\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:5415:7862\t748449\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:13091:8089\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:2775:8182\t77133\t465\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:20859:8468\t77133\t465\tQ:1\n-C\tM02'..b'7:10742\t155900\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2111:17410:14873\t155900\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2111:8468:18351\t48479\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:24696:4765\t48479\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:22908:11568\t155900\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:21677:11616\t48479\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:18610:13959\t155900\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:29322:14357\t48479\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:27932:17861\t155900\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:19386:19350\t155900\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2116:20842:13805\t2\t428\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1108:24933:8836\t48479\t427\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1115:20021:13386\t77133\t427\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:11257:15569\t155900\t427\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2116:11149:14851\t2\t427\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:26359:6612\t77133\t426\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2107:23381:21230\t2\t426\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2116:28230:13317\t2\t426\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1115:6735:7878\t48479\t425\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2116:8949:21310\t2\t425\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:5542:10375\t136703\t424\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2104:18472:17579\t77133\t422\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2108:21119:13984\t77133\t421\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1102:19274:12249\t2\t420\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:23634:15417\t2\t419\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:26128:7305\t77133\t419\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2104:7439:6865\t77133\t419\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2113:9450:7860\t77133\t419\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1105:24157:12563\t171549\t418\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2109:6096:10827\t77133\t417\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:13543:15586\t2\t415\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2116:12509:10049\t48479\t415\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2118:26456:13140\t2\t414\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1105:13117:20051\t77133\t412\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2105:27848:11057\t77133\t407\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2109:14547:16056\t77133\t407\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2116:8415:20212\t2\t400\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2111:13059:9985\t77133\t398\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:11218:18482\t2\t394\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1108:23719:8436\t2\t393\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2112:9415:20030\t2\t392\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2105:24502:18789\t77133\t391\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2104:19106:20150\t2\t388\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2110:6159:5038\t77133\t384\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2107:28345:16458\t2\t374\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2105:15748:20757\t77133\t373\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2110:4035:5602\t152509\t367\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2112:10518:18769\t155900\t359\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2111:13968:11139\t2\t352\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2111:24542:14435\t77133\t344\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1119:23951:3621\t2\t316\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1108:12019:7678\t77133\t228\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1103:15691:18080\t77133\t167\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1114:15782:7171\t77133\t167\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1116:26163:21828\t1654\t167\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1101:16009:8262\t77133\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:4948:9359\t77133\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:7127:11365\t2\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1108:7315:10840\t77133\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1108:22055:17293\t2\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1117:8041:5693\t77133\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1117:22456:10966\t2\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1117:24299:12438\t2\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1119:17233:7295\t2\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1119:16223:13539\t77133\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:2101:15742:10457\t2\t166\tQ:1\n-C\tM02286:29:000000000-AA53D:1:1104:13419:19934\t77133\t163\tQ:1\n' |
| b |
| diff -r f03c7ba8d8bc -r 50bd98b3ae5a test-data/ncbi_taxonomy.loc.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncbi_taxonomy.loc.test Fri Sep 29 14:38:33 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#value #name path +test test ${__HERE__}/tax_dir |
| b |
| diff -r f03c7ba8d8bc -r 50bd98b3ae5a test-data/tax_dir/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tax_dir/names.dmp Fri Sep 29 14:38:33 2023 +0000 |
| b |
| @@ -0,0 +1,20 @@ +1 | all | | synonym | +1 | root | | scientific name | +2 | Bacteria | Bacteria <prokaryote> | scientific name | +2 | Monera | Monera <Bacteria> | in-part | +2 | Procaryotae | Procaryotae <Bacteria> | in-part | +2 | Prokaryota | Prokaryota <Bacteria> | in-part | +2 | Prokaryotae | Prokaryotae <Bacteria> | in-part | +2 | bacteria | bacteria <blast2> | blast name | +2 | eubacteria | | genbank common name | +2 | not Bacteria Haeckel 1894 | | synonym | +2 | prokaryote | prokaryote <Bacteria> | in-part | +2 | prokaryotes | prokaryotes <Bacteria> | in-part | +6 | Azorhizobium | | scientific name | +6 | Azorhizobium Dreyfus et al. 1988 emend. Lang et al. 2013 | | authority | +6 | Azotirhizobium | | misspelling | +7 | ATCC 43989 | | type material | +7 | Azorhizobium caulinodans | | scientific name | +7 | Azorhizobium caulinodans Dreyfus et al. 1988 | | synonym | +7 | Azotirhizobium caulinodans | | equivalent name | +7 | CCUG 26647 | | type material | |
| b |
| diff -r f03c7ba8d8bc -r 50bd98b3ae5a test-data/tax_dir/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tax_dir/nodes.dmp Fri Sep 29 14:38:33 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +2 | 2 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +6 | 6 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +7 | 7 | species | AC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | |
| b |
| diff -r f03c7ba8d8bc -r 50bd98b3ae5a tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Sep 29 14:38:33 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Kraken database in the required format --> + <table name="ncbi_taxonomy" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/ncbi_taxonomy.loc.test" /> + </table> +</tables> |