Mercurial > repos > devteam > kraken_translate
changeset 4:9a5be5b1a5c9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
| author | iuc |
|---|---|
| date | Wed, 04 Dec 2019 06:51:08 -0500 |
| parents | 9bdcba262627 |
| children | bc3e90fd13be |
| files | kraken-translate.xml macros.xml test-data/kraken-translate/kraken_translate_test1.tab test-data/kraken-translate/kraken_translate_test1_output.tab test-data/kraken-translate/test_database.loc 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/kraken_databases.loc.sample |
| diffstat | 13 files changed, 57 insertions(+), 100 deletions(-) [+] |
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--- a/kraken-translate.xml Mon Aug 07 17:29:45 2017 -0400 +++ b/kraken-translate.xml Wed Dec 04 06:51:08 2019 -0500 @@ -27,10 +27,10 @@ </outputs> <tests> <test> - <param name="input" value="kraken_translate_test1.tab" ftype="tabular"/> + <param name="input" value="kraken-translate/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"/> + <param name="kraken_database" value="new_style_test_entry"/> + <output name="translated" file="kraken-translate/kraken_translate_test1_output.tab" ftype="tabular"/> </test> </tests> <help><![CDATA[
--- a/macros.xml Mon Aug 07 17:29:45 2017 -0400 +++ b/macros.xml Wed Dec 04 06:51:08 2019 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">1.2.3</token> + <token name="@WRAPPER_VERSION@">1.3.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement> + <requirement type="package" version="1.1.1">kraken</requirement> </requirements> </xml> <xml name="version_command"> @@ -23,6 +23,10 @@ <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations> </xml> - <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token> - <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token> + <!-- See the kraken_databases.loc.sample documentation, + this if statement is for backward compatibility as early + versions of the wrapper assumed the UI facing field name + was also part of the directory path --> + <token name="@SET_DATABASE_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</token> + <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token> </macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-translate/kraken_translate_test1.tab Wed Dec 04 06:51:08 2019 -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-translate/kraken_translate_test1_output.tab Wed Dec 04 06:51:08 2019 -0500 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken-translate/test_database.loc Wed Dec 04 06:51:08 2019 -0500 @@ -0,0 +1,20 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the Kraken DB) +# +# Modern usage assumes $path is the folder containing +# the Kraken database of interest: +# +new_style_test_entry "Test Database" ${__HERE__}/test_db + +# The kraken wrapper still supports an alternative +# legacy usage where $path/$name is the folder +# containing the Kraken database of interest, meaning +# $name must be both a folder name and human readable +# description of the DB to show in the Galaxy UI: +old_style_test_entry test_db ${__HERE__} + +# NOTE: This legacy style should be avoided as other +# tools also using the kraken_database.loc file may +# not understand it!
--- a/test-data/kraken_translate_test1.tab Mon Aug 07 17:29:45 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
--- a/test-data/kraken_translate_test1_output.tab Mon Aug 07 17:29:45 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -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
--- a/test-data/test_database.loc Mon Aug 07 17:29:45 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
--- a/test-data/test_db/taxonomy/names.dmp Mon Aug 07 17:29:45 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<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 |
--- a/test-data/test_db/taxonomy/nodes.dmp Mon Aug 07 17:29:45 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 | |
--- a/tool-data/kraken_databases.loc.sample Mon Aug 07 17:29:45 2017 -0400 +++ b/tool-data/kraken_databases.loc.sample Wed Dec 04 06:51:08 2019 -0500 @@ -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. +# plants2018<tab>Plant genomes (2018)<tab>/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. +# plants2018<tab>plants_2018<tab>/path/to/krakenDB +# +# Please avoid this legacy usage, as not all tools using +# the kraken_databases.loc file will understand it.