| Previous changeset 0:77ca66b1f5e9 (2015-07-23) Next changeset 2:b9971bca4b01 (2016-03-23) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 3abfc7eb2999fa588862b84c453012c811fa8350 |
|
modified:
kraken-translate.xml macros.xml tool_dependencies.xml |
|
added:
test-data/kraken_translate_test1.tab test-data/kraken_translate_test1_output.tab test-data/test_database.loc test-data/test_db/database.idx test-data/test_db/database.kdb test-data/test_db/taxonomy/names.dmp test-data/test_db/taxonomy/nodes.dmp tool_data_table_conf.xml.test |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 kraken-translate.xml --- a/kraken-translate.xml Thu Jul 23 10:56:31 2015 -0400 +++ b/kraken-translate.xml Mon Mar 21 12:07:33 2016 -0400 |
| [ |
| @@ -1,10 +1,13 @@ -<tool id="kraken-translate" name="Kraken-translate" version="1.1.0"> +<tool id="kraken-translate" name="Kraken-translate" version="1.2.0"> <description> convert taxonomy IDs to names </description> <macros> <import>macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> <command> <![CDATA[ @SET_DATABASE_PATH@ && @@ -19,6 +22,14 @@ <outputs> <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" /> </outputs> + <tests> + <test> + <param name="input" value="kraken_translate_test1.tab" ftype="tabular"/> + <param name="mpa-format" value="false"/> + <param name="kraken_database" value="test_db"/> + <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/> + </test> + </tests> <help> <![CDATA[ @@ -45,8 +56,5 @@ Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate. ]]> </help> - <expand macro="requirements" /> - <expand macro="stdio" /> - <expand macro="version_command" /> <expand macro="citations" /> </tool> |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 macros.xml --- a/macros.xml Thu Jul 23 10:56:31 2015 -0400 +++ b/macros.xml Mon Mar 21 12:07:33 2016 -0400 |
| b |
| @@ -2,7 +2,10 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.10.5">kraken</requirement> + <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement> + </requirements> + <requirements> + <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement> </requirements> </xml> <xml name="stdio"> |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 test-data/kraken_translate_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_translate_test1.tab Mon Mar 21 12:07:33 2016 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 test-data/kraken_translate_test1_output.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_translate_test1_output.tab Mon Mar 21 12:07:33 2016 -0400 |
| b |
| @@ -0,0 +1,4 @@ +gi|145231|gb|M33724.1|ECOALPHOA root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12 +gi|145232|gb|M33725.1|ECOALPHOB root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12 +gi|145234|gb|M33727.1|ECOALPHOE root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12 +gi|146195|gb|J01619.1|ECOGLTA root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli;Escherichia coli K-12 |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 test-data/test_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_database.loc Mon Mar 21 12:07:33 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +test_db test_db ${__HERE__} \ No newline at end of file |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 test-data/test_db/database.idx |
| b |
| Binary file test-data/test_db/database.idx has changed |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 test-data/test_db/database.kdb |
| b |
| Binary file test-data/test_db/database.kdb has changed |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 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 12:07:33 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<blast91347> | 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<blast1236> | 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<blast1224> | 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 <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 | +1 | all | | synonym | +1 | root | | scientific name | +131567 | biota | | synonym | +131567 | cellular organisms | | scientific name | |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 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 12:07:33 2016 -0400 |
| b |
| @@ -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 | | |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 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 12:07:33 2016 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Kraken database in the required format --> + <table name="kraken_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/test_database.loc" /> + </table> +</tables> |
| b |
| diff -r 77ca66b1f5e9 -r 475284b74179 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jul 23 10:56:31 2015 -0400 +++ b/tool_dependencies.xml Mon Mar 21 12:07:33 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="kraken" version="0.10.5"> - <repository changeset_revision="89a36b0f718c" name="package_kraken_0_10_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="kraken" version="0.10.6-eaf8fb68"> + <repository changeset_revision="0743afe4dcb8" name="package_kraken_0_10_6_eaf8fb68" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |