# HG changeset patch # User iuc # Date 1576011934 18000 # Node ID 11a61934bfb385f2e37676b22bb134231191cb0b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit 863ad85836c80811d1d6b82eaf3ce903b273368a" diff -r 000000000000 -r 11a61934bfb3 cat_contigs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cat_contigs.xml Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,92 @@ + + annotate with taxonomic classification + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 11a61934bfb3 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,389 @@ + + 5.0.3 + + + cat + + + + + + + CAT_database + taxonomy + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + predicted_proteins.faa and alignment.diamond from previous CAT run. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${__tool_directory__}/tabpad.py + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 'log' in select_outputs or not select_outputs + + + 'predicted_proteins_faa' in select_outputs and previous['use_previous'] == 'no' + + + 'predicted_proteins_gff' in select_outputs and previous['use_previous'] == 'no' + + + 'alignment_diamond' in select_outputs and previous['use_previous'] == 'no' + + + + + + + 'orf2lca' in select_outputs + + + + + + + 'contig2classification' in select_outputs + + + + + + + 'bin2classification' in select_outputs + + + + + + + names['add_names'] in ['both','orf2lca'] + + + + + + + names['add_names'] in ['both','classification'] + + + + + + + 'classification' in summarise + + + + + + + + + + + + + https://doi.org/10.1101/072868 + https://doi.org/10.1186/s13059-019-1817-x + https://doi.org/10.1038/nmeth.3176 + https://doi.org/10.1186/1471-2105-11-119 + + + + diff -r 000000000000 -r 11a61934bfb3 tabpad.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tabpad.py Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,67 @@ +#!/usr/bin/env python + +import argparse +import re + + +def padfile(infile, outfile, fieldcnt=None): + with open(infile, 'r') as fh: + out = open(outfile, 'w') + commentlines = [] + tabs = '\t' * fieldcnt if fieldcnt is not None else None + + def pad_line(txtline, tabs=None): + line = txtline.rstrip('\r\n') + fields = line.split('\t') + if not tabs: + tabs = '\t' * len(fields) + out.write('%s%s\n' % (line, tabs[len(fields):])) + + for i, txtline in enumerate(fh): + if txtline.lstrip().startswith('#'): + commentlines.append(txtline) + else: + if commentlines: + for i in range(len(commentlines) - 1): + out.write(commentlines[i]) + pad_line(commentlines[-1], tabs=tabs) + commentlines = [] + pad_line(txtline, tabs=tabs) + out.close() + + +def fieldcount(infile): + fieldcnt = 0 + with open(infile, 'r') as fh: + for i, line in enumerate(fh): + fieldcnt = max(fieldcnt, len(line.rstrip('\r\n').split('\t'))) + return fieldcnt + + +def tsvname(infile): + return re.sub('.txt$', '', infile) + '.tsv' + + +def __main__(): + parser = argparse.ArgumentParser( + description='Pad a file with TABS for equal field size across lines') + parser.add_argument( + '-i', '--input', help='input file') + parser.add_argument( + '-o', '--output', help='output file') + parser.add_argument( + 'files', nargs='*', help='.txt files') + args = parser.parse_args() + + if args.input: + outfile = args.output if args.output else tsvname(args.input) + fieldcnt = fieldcount(args.input) + padfile(args.input, outfile, fieldcnt=fieldcnt) + for infile in args.files: + outfile = tsvname(infile) + fieldcnt = fieldcount(infile) + padfile(infile, outfile, fieldcnt=fieldcnt) + + +if __name__ == "__main__": + __main__() diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.dmnd Binary file test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.dmnd has changed diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.fastaid2LCAtaxid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.fastaid2LCAtaxid Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,10 @@ +WP_000159554.1 2 +WP_000214552.1 91061 +WP_000346214.1 91061 +WP_000568619.1 666 +WP_000958804.1 1301 +WP_000991933.1 666 +WP_000996146.1 666 +WP_003722398.1 1639 +WP_005378126.1 662 +XP_961517.1 5141 diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.gz Binary file test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.gz has changed diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.taxids_with_multiple_offspring --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/CAT_prepare_test/CAT_database/test.nr.taxids_with_multiple_offspring Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,17 @@ +91061 +1 +641 +1224 +1236 +131567 +1637 +1639 +1783272 +2 +662 +13562 +13562 +641 +662 +666 +91061 diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/taxonomy/names.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/CAT_prepare_test/taxonomy/names.dmp Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,252 @@ +1 | all | | synonym | +1 | root | | scientific 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 | prokaryote | prokaryote | in-part | +2 | prokaryotes | prokaryotes | in-part | +641 | Vibrionaceae | | scientific name | +641 | Vibrionaceae Veron 1965 | | authority | +641 | gamma-3 proteobacteria | gamma-3 proteobacteria <#3> | in-part | +662 | "Microspira" Schroeter 1886 | | authority | +662 | "Pacinia" Trevisan 1885 | | authority | +662 | Beneckea | | synonym | +662 | Beneckea Campbell 1957 | | authority | +662 | Listonella | | synonym | +662 | Listonella MacDonell and Colwell 1986 | | authority | +662 | Microspira | | synonym | +662 | Pacinia | | synonym | +662 | Vibrio | | scientific name | +662 | Vibrio Pacini 1854 | | authority | +666 | "Bacillo virgola del Koch" Trevisan 1884 | | authority | +666 | "Bacillus cholerae" (Pacini 1854) Trevisan 1884 | | authority | +666 | "Bacillus cholerae-asiaticae" Trevisan 1884 | | authority | +666 | "Kommabacillus" Koch 1884 | | authority | +666 | "Liquidivibrio cholerae" (Pacini 1854) Orla-Jensen 1909 | | authority | +666 | "Microspira comma" Schroeter 1886 | | authority | +666 | "Pacinia cholerae-asiaticae" (Trevisan 1884) Trevisan 1885 | | authority | +666 | "Spirillum cholerae" (Pacini 1854) Mac1889 | | authority | +666 | "Spirillum cholerae-asiaticae" (Trevisan 1884) Zopf 1885 | | authority | +666 | "Vibrio cholera" (sic) Pacini 1854 | | authority | +666 | "Vibrio cholerae-asiaticae" (Trevisan 1884) Pfeiffer 1896 | | authority | +666 | "Vibrio comma" (Schroeter 1886) Blanchard 1906 | | authority | +666 | ATCC 14035 | ATCC 14035 | type material | +666 | ATCC 14547 [[Vibrio albensis]] | ATCC 14547 [[Vibrio albensis]] | type material | +666 | Bacillo virgola del Koch | | synonym | +666 | Bacillus cholerae | | synonym | +666 | Bacillus cholerae-asiaticae | | synonym | +666 | CCUG 48664 [[Vibrio albensis]] | CCUG 48664 [[Vibrio albensis]] | type material | +666 | CCUG 9118 A | CCUG 9118 A | type material | +666 | CECT 514 | CECT 514 | type material | +666 | CIP 62.13 | CIP 62.13 | type material | +666 | Kommabacillus | | synonym | +666 | LMG 4406 [[Vibrio albensis]] | LMG 4406 [[Vibrio albensis]] | type material | +666 | LMG:4406 [[Vibrio albensis]] | LMG:4406 [[Vibrio albensis]] | type material | +666 | Liquidivibrio cholerae | | synonym | +666 | Microspira comma | | synonym | +666 | NCIMB 41 [[Vibrio albensis]] | NCIMB 41 [[Vibrio albensis]] | type material | +666 | NCTC 8021 | NCTC 8021 | type material | +666 | Pacinia cholerae-asiaticae | | synonym | +666 | Spirillum cholerae | | synonym | +666 | Spirillum cholerae-asiaticae | | synonym | +666 | Vibrio albensis | | synonym | +666 | Vibrio albensis Lehmann and Neumann 1896 | | authority | +666 | Vibrio cholera | | synonym | +666 | Vibrio cholerae | | scientific name | +666 | Vibrio cholerae Pacini 1854 | | authority | +666 | Vibrio cholerae biovar albensis | | synonym | +666 | Vibrio cholerae bv. albensis | | synonym | +666 | Vibrio cholerae-asiaticae | | synonym | +666 | Vibrio comma | | synonym | +1224 | Alphaproteobacteraeota | | synonym | +1224 | Alphaproteobacteraeota Oren et al. 2015 | | authority | +1224 | Alphaproteobacteriota | | synonym | +1224 | Proteobacteria | | scientific name | +1224 | Proteobacteria Garrity et al. 2005 | | authority | +1224 | Proteobacteria [class] Stackebrandt et al. 1988 | | 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 | +1236 | Gammaproteobacteria | | scientific name | +1236 | Gammaproteobacteria Garrity et al. 2005 emend. Williams and Kelly 2013 | | authority | +1236 | Proteobacteria gamma subdivision | | synonym | +1236 | Purple bacteria, gamma subdivision | | synonym | +1236 | g-proteobacteria | | blast name | +1236 | gamma proteobacteria | | synonym | +1236 | gamma subdivision | | synonym | +1236 | gamma subgroup | | synonym | +1239 | Bacillaeota | | synonym | +1239 | Bacillaeota Oren et al. 2015 | | authority | +1239 | Bacillota | | synonym | +1239 | Bacillus/Clostridium group | | synonym | +1239 | Clostridium group firmicutes | | synonym | +1239 | Firmacutes | | synonym | +1239 | Firmicutes | | scientific name | +1239 | Firmicutes corrig. Gibbons and Murray 1978 | | authority | +1239 | Low G+C firmicutes | | synonym | +1239 | clostridial firmicutes | | synonym | +1239 | firmicutes | firmicutes | blast name | +1239 | low G+C Gram-positive bacteria | | common name | +1239 | low GC Gram+ | | common name | +1385 | Bacillales | | scientific name | +1385 | Bacillales Prevot 1953 | | authority | +1385 | Bacillus/Staphylococcus group | | synonym | +1637 | "Listerella" Pirie 1927 (nom. rej. Opin. 14) | | authority | +1637 | Listerella | | synonym | +1637 | Listeria | | scientific name | +1637 | Listeria Pirie 1940 | | authority | +1639 | "Bacterium monocytogenes hominis" Nyfeldt 1932 | | authority | +1639 | "Bacterium monocytogenes" Murray et al. 1926 | | authority | +1639 | "Corynebacterium infantisepticum" Potel 1950 | | authority | +1639 | "Corynebacterium parvulum" Schultz et al. 1934 | | authority | +1639 | "Erysipelothrix monocytogenes" (Murray et al. 1926) Wilson and Miles 1946 | | authority | +1639 | "Listerella hepatolytica" Pirie 1927 | | authority | +1639 | ATCC 15313 | ATCC 15313 | type material | +1639 | Bacterium monocytogenes | | synonym | +1639 | Bacterium monocytogenes hominis | | synonym | +1639 | CCUG 15526 | CCUG 15526 | type material | +1639 | CIP 82.110 | CIP 82.110 | type material | +1639 | Corynebacterium infantisepticum | | synonym | +1639 | Corynebacterium parvulum | | synonym | +1639 | DSM 20600 | DSM 20600 | type material | +1639 | Erysipelothrix monocytogenes | | synonym | +1639 | Listerella hepatolytica | | synonym | +1639 | Listeria monocytogenes | | scientific name | +1639 | Listeria monocytogenes (Murray et al. 1926) Pirie 1940 | | authority | +1639 | Listeria sp. FDA00013359 | | includes | +1639 | Listeria sp. FDA00013360 | | includes | +1639 | Listeria sp. FDA00013361 | | includes | +1639 | Listeria sp. FDA00013362 | | includes | +1639 | Listeria sp. FDA00013363 | | includes | +1639 | Listeria sp. FDA00013364 | | includes | +1639 | Listeria sp. FDA00013365 | | includes | +1639 | Listeria sp. FDA00013366 | | includes | +1639 | Listeria sp. FDA00013367 | | includes | +1639 | Listeria sp. FDA00013503 | | includes | +1639 | Listeria sp. FDA00013504 | | includes | +1639 | Listeria sp. FDA00013505 | | includes | +1639 | Listeria sp. FDA00013506 | | includes | +1639 | Listeria sp. FDA00013507 | | includes | +1639 | Listeria sp. FDA00013508 | | includes | +1639 | Listeria sp. FDA00013509 | | includes | +1639 | Listeria sp. FDA00013510 | | includes | +1639 | Listeria sp. FDA00013511 | | includes | +1639 | Listeria sp. FDA00013512 | | includes | +1639 | Listeria sp. FDA00013536 | | includes | +1639 | Listeria sp. FDA00013537 | | includes | +1639 | Listeria sp. FDA00013538 | | includes | +1639 | Listeria sp. FDA00013539 | | includes | +1639 | Listeria sp. FDA00013540 | | includes | +1639 | Listeria sp. FDA00013541 | | includes | +1639 | Listeria sp. FDA00013542 | | includes | +1639 | Listeria sp. FDA00013543 | | includes | +1639 | Listeria sp. FDA00013544 | | includes | +1639 | Listeria sp. FDA00013545 | | includes | +1639 | Listeria sp. FDA00013546 | | includes | +1639 | Listeria sp. FDA00013547 | | includes | +1639 | Listeria sp. FDA00013548 | | includes | +1639 | Listeria sp. FDA00013549 | | includes | +1639 | Listeria sp. FDA00013550 | | includes | +1639 | Listeria sp. FDA00013551 | | includes | +1639 | Listeria sp. FDA00013552 | | includes | +1639 | Listeria sp. FDA00013553 | | includes | +1639 | Listeria sp. FDA00013554 | | includes | +1639 | Listeria sp. FDA00013555 | | includes | +1639 | Listeria sp. FDA00013556 | | includes | +1639 | Listeria sp. FDA00013557 | | includes | +1639 | Listeria sp. FDA00013558 | | includes | +1639 | Listeria sp. FDA00013559 | | includes | +1639 | Listeria sp. FDA00013560 | | includes | +1639 | Listeria sp. FDA00013561 | | includes | +1639 | Listeria sp. FDA00013562 | | includes | +1639 | Listeria sp. FDA00013563 | | includes | +1639 | Listeria sp. FDA00013564 | | includes | +1639 | Listeria sp. FDA00013565 | | includes | +1639 | Listeria sp. FDA00013566 | | includes | +1639 | Listeria sp. FDA00013567 | | includes | +1639 | Listeria sp. FDA00013568 | | includes | +1639 | Listeria sp. FDA00013570 | | includes | +1639 | Listeria sp. FDA00013571 | | includes | +1639 | Listeria sp. FDA00013572 | | includes | +1639 | Listeria sp. FDA00013573 | | includes | +1639 | Listeria sp. FDA00013574 | | includes | +1639 | Listeria sp. FDA00013575 | | includes | +1639 | Listeria sp. FDA00013576 | | includes | +1639 | Listeria sp. FDA00013577 | | includes | +1639 | Listeria sp. FDA00013578 | | includes | +1639 | Listeria sp. FDA00013579 | | includes | +1639 | Listeria sp. FDA00013607 | | includes | +1639 | NCTC 10357 | NCTC 10357 | type material | +1639 | SLCC 53 | SLCC 53 | type material | +2157 | "Archaea" Woese et al. 1990 | | authority | +2157 | "Archaebacteria" (sic) Woese and Fox 1977 | | authority | +2157 | Archaea | | scientific name | +2157 | Archaebacteria | | synonym | +2157 | Mendosicutes | | synonym | +2157 | Metabacteria | | synonym | +2157 | Monera | Monera | in-part | +2157 | Procaryotae | Procaryotae | in-part | +2157 | Prokaryota | Prokaryota | in-part | +2157 | Prokaryotae | Prokaryotae | in-part | +2157 | archaea | archaea | blast name | +2157 | prokaryote | prokaryote | in-part | +2157 | prokaryotes | prokaryotes | in-part | +2158 | Methanobacteriales | | scientific name | +2158 | Methanobacteriales Balch and Wolfe 1981 | | authority | +2159 | Methanobacteriaceae | | scientific name | +2159 | Methanobacteriaceae Barker 1956 | | authority | +2172 | Methanobrevibacter | | scientific name | +2172 | Methanobrevibacter Balch and Wolfe 1981 | | authority | +28890 | "Euryarchaeota" Woese et al. 1990 | | authority | +28890 | Euryarchaeota | | scientific name | +28890 | Euryarchaeota Garrity and Holt 2002 | | authority | +28890 | Methanobacteraeota | | synonym | +28890 | Methanobacteraeota Oren et al. 2015 | | authority | +28890 | Methanobacteriota | | synonym | +28890 | euryarchaeotes | euryarchaeotes | blast name | +83816 | ATCC 35063 | ATCC 35063 | type material | +83816 | DSM 1093 | DSM 1093 | type material | +83816 | JCM 13430 | JCM 13430 | type material | +83816 | Methanobacterium ruminantium | | synonym | +83816 | Methanobacterium ruminantium Smith and Hungate 1958 (Approved Lists 1980) | | authority | +83816 | Methanobrevibacter ruminantium | | scientific name | +83816 | Methanobrevibacter ruminantium (Smith and Hungate 1958) Balch and Wolfe 1981 | | authority | +83816 | OCM 146 | OCM 146 | type material | +83816 | strain M1 | strain M1 | type material | +91061 | Bacilli | | scientific name | +91061 | Bacilli Ludwig et al. 2010 | | authority | +91061 | Bacillus/Lactobacillus/Streptococcus group | | synonym | +91061 | Firmibacteria | | synonym | +91061 | Firmibacteria Murray 1988 | | authority | +131567 | biota | | synonym | +131567 | cellular organisms | | scientific name | +135623 | 'Vibrionales' | | synonym | +135623 | Vibrionaceae group | | synonym | +135623 | Vibrionales | | scientific name | +183925 | Archaeobacteria | | synonym | +183925 | Archaeobacteria Murray 1988 | | authority | +183925 | Methanobacteria | | scientific name | +183925 | Methanobacteria Boone 2002 | | authority | +183967 | Thermoplasmata | | scientific name | +183967 | Thermoplasmata Reysenbach 2002 | | authority | +186820 | Listeriaceae | | scientific name | +186820 | Listeriaceae Ludwig et al. 2010 | | authority | +1235850 | "Methanoplasmatales" Paul et al. 2012 | | authority | +1235850 | Methanomassiliicoccales | | scientific name | +1235850 | Methanomassiliicoccales Iino et al. 2013 | | authority | +1235850 | Methanoplasmatales | | synonym | +1783272 | Terrabacteria group | | scientific name | +2283794 | "Methanomada" Petitjean et al. 2015 | | authority | +2283794 | Methanogen Class I | | synonym | +2283794 | Methanomada | | equivalent name | +2283794 | Methanomada group | | scientific name | +2283796 | Diaforarchaea | | equivalent name | +2283796 | Diaforarchaea Petijean et al. 2015 | | authority | +2283796 | Diaforarchaea group | | scientific name | diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/taxonomy/nodes.dmp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/CAT_prepare_test/taxonomy/nodes.dmp Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,27 @@ +1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | +2 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +641 | 135623 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +662 | 641 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +666 | 662 | species | VC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +1224 | 2 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1236 | 1224 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1239 | 1783272 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1385 | 91061 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1637 | 186820 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1639 | 1637 | species | LM | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +2157 | 131567 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | +2158 | 183925 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2159 | 2158 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2172 | 2159 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +28890 | 2157 | phylum | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +83816 | 2172 | species | MR | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +91061 | 1239 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +131567 | 1 | no rank | | 8 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | | +135623 | 1236 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +183925 | 2283794 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +183967 | 2283796 | class | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +186820 | 1385 | family | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1235850 | 183967 | order | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +1783272 | 2 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | +2283794 | 28890 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | +2283796 | 28890 | no rank | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/CAT_prepare_test/taxonomy/test.prot.accession2taxid.gz Binary file test-data/cached_locally/CAT_prepare_test/taxonomy/test.prot.accession2taxid.gz has changed diff -r 000000000000 -r 11a61934bfb3 test-data/cached_locally/cat_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/cat_database.loc Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,8 @@ +## A typical download from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz +# ls CAT_prepare_20190719/ +# 2019-07-19.CAT_prepare.fresh.log +# 2019-07-19_CAT_database +# 2019-07-19_taxonomy +#value name database_folder taxonomy_folder +#2019-07-19_CAT_database 2019-07-19_CAT_database /opt/galaxy/tool-data/cat_database/CAT_prepare_20190719/2019-07-19_CAT_database /opt/galaxy/tool-data/cat_database/CAT_prepare_20190719/2019-07-19_taxonomy +CAT_prepare_test CAT_prepare_test ${__HERE__}/CAT_prepare_test/CAT_database ${__HERE__}/CAT_prepare_test/taxonomy diff -r 000000000000 -r 11a61934bfb3 test-data/contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.fasta Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,93 @@ +>contig_9952 +TGGTTATGTACGCAGACAGCTTACTCCTCCTCGGAGACCACTCGCGGTACTCTATTCCCTCCACGGTTGCGAGGCGCTCGCCGTAGATCCGCTTCCCGGG +ACAGGCAGACAGGGTGTATAGCCTCCCCCTCTCGGAAAAAACCCCGGGCACGCGGTCCAAAGACTCCATGCCCGTAACAACGCCGTGGTTTTAGAAATAA +TCTGTGCCGTCGGTTGCAAACCCTAAATACAGGGGGATATCAATGCGGTTGCATGGATATCCACATCCTTCGTGAGATCGCCGACGCAGTTCAGGCGGCG +GTATCTCTCATACCCGACCCCTGCAGCAGGGGCAACGAGATATGCATGGGCAACGACGGCACACCCACATCCGAGATAGACAAAGTGGCTGAGAACGCGG +TGCTCGGGTACATAGAGTCCAACCGCCTGGCTCTGAACGTGCTCAGCGAAGAGATAGGCTTCGTGGACAACGGCGCGTCGGAGGTTCTGGTCCTCGATCC +CATCGATGGGACAAGCAATTCAGTGGCCGAGATACCTTTCTATACGATATCCATGGCCGTCGGCAAGGATTCGCTCTGCGGCATGCACACGGCCTACATC +AGGAACCTGGCGACAGGGGACGAGTTCTGGGCGCACAAAGGGGATGGCGCTTATTACAACGGAAGGAGGATAAACGTCAGGAAGCCGGATTTCTCCAAAC +TGTTCGCCCTTATATACATGGGGAACGCCGCTGTCGATGAAGCGTTCGCCCTTGCAAAGAACGTCAAGACCTCCCGCTCCATGGGCTGCGCCTCCCTTGA +GATGACGCTCGTGGCACTAGGACACGCCGATATCTATTACATGAACACCTACCGTTACAACCGTGCCGTCAGGACTGTGGACATCGCCGCCAGCGCCCTG +ATACTCAGGGAGGCGGGCGGCGAGATATTCGATATCGGCGGCAACAAGCTGGATATGCCGCTGGACAACGCTTACCACGCAAGCTTCGTGGCGTGCTCCT +GCAAAGAGGTATTCGACCACATCATGAGGGCCCACATCGAGGAGCACGGCGCTACGCGTTACGGGATATACGCCAACGAGACCGTCCCCGGGGCGGCCGA +GTATGTGAGGAGGGCGTACGATGCTTTGAGGGGGGAGAAGGTAACCCTCGACACGGCGGCCGCCAGGCTGATCGGGGCGGAAGGCGTGCCTATTTCGGAG +ATCGAGGCGGACATCGTCGTGGTGATAGGAGGGGACGGCACGATACTCAGGGCGCTCAAGAAGACGGATGCCGCCGTGATAGGGATCAACGCCGGAGGCG +TGGGGTTCCTGGCCGAGGTCGAGCCGGACGAGATAGAGGAGAGCATATCCCGCATCAGGCGCGGAGAGTACTCGGTTGAGGAGAGGATCAAGCTCAGGAC +TTTTTACGAGGGGGAATATCTCTCGGAGGCCGTGAACGAGACAGTGATACACACTGATTCCGTGGCGAAGATCAGGCAGTTCAAGATATATGTCAACGAA +CACCTGGCAACGGAGGTCCGCGCGGACGGCATAATCATCTCGACGCCCACAGGCTCCACCTGCTACGCCATGAGCCTCGGCGCGCCCATAACCGACCCGG +GGGTCGGAGCTTTCCTGATAGTCCCCATGGCGGCGTTCAAGTTCGCTTCCCGTCCGTTCGTCGTTCCCTATACGGCGAAGATAACCGTCGAGGCGGTCAT +GGACAAGGGCTGCCTCATCGTGGTGGACGGCCAGCACGAGTACCCGATGAGGGGAGGGACGCGGGCGGAATTCTCGCTTTCCGACAACCTCGCCAAATTC +TCGGCCCCGGCGTTCCTGGCATCGACGGGCATCTCGAAGTAGATCTCGCCGCCCATCATGTTGATGTCGGCCTTAAAAGGTAAAGAAAGCCAGATGGCGT +TCGAGACATCGGAGTCGTCCAGCTCGGCGAAGTAATCGCCGCTCGTCGTGACAATCTTCATTCTGCTCAAAGCGCCACCCGGCCGTCGGTTCAGTTCTTT +TTCTTCTTTTCGAAGAGCTTCCTGATCTCCCTGCCCGTGACCTCGATCTGGAGGTCCTTCTCCTTCTCCTCCATTGCCTTCAGGCCCTTCAGGTCGTTGG +CCCATTCGGAGGTCCAGTCGGCTTTGAATTTTCCGGATTCGATGTCGTCCAGAATCTTCTTCATGCCCTTCTCGGACTCTTCGGTGATCACCAGGTCCCT +CCTGGTAAGGCCTCCGTACTCGGCAGTGTTGGAAACGACGTGCCACATCTTCTCGAAACCGCCCTCGTTTATGAGGTCGACGATGAGCTTCGCCTCATGG +CATACTTCGAAGTAGGCCATTTCGGGAGGGTATCCTCCCTCGACCAGGGTCTTGAATCCCGACTTTATGAGGCCGGTGGTCCCTCCGCACAGCACGGCCT +GCTCTCCGAACAGGTCTGTGAGCGTCTCGTTGTCGAAAGTGGTCTCGAAGACGCCGGCGCGGGTGGCTCCGAGCCCCTTTGCAAGTGCAAGGGCGATCTT +CTTGGCGTTGCCGGTATAGTCCTGGTGGACGCAAACGAGGGCCGGAACTCCGAATCCCTCGACGAACACATCCCTTTCTTTGTCCCCGGGGGCCTTGGGA +GCCATCATTATGACGTCGATGTTTTTCGGAGGAACGATGGTCTTGTAGGTCACAGCGAAACCGTGGGCGAACTCAAGTGCGCAGCCCTCCCTGATGTTGG +GCTCGACGAATTCTTTGTATACCTTTGGCTGGACCTCGTCGGGCAGAAGCATCATGATGACGTCCGCGGTCTTGGCGGCCTCGGCGAAATCTACGACCTT +GAAGCCGTCCTCTTTCGCTTTGTTCCATGATCTTCCGTCTTTCCTGAGCCCGATCACTACGTTGAGGCCGGAGTCCCTGAAGCACAGGGCCTGCGCTCTC +CCCTGGGATCCGTAGCCCATGACGGCGACCGTTTTTCCTTTAAGGACATCTATGTCCACATCTGCATCGTGGTAAATCTTCATTATATCCACCTGTTTAG +AGGTCCAACTGCTTTATAGACTAAAAGGTATCGTTCCCGCTCCGACATATAGGTCAGTTCAGTACTGGCAGCGTCCTTTGACCAGGGCCTGATTCGGATT +GGCAGGCAGCATGGGCAACACGTCCTCCTCGGGATCGATGTGGATGTCCAGCAGGCACGTCTCGCCGCTGTCTATTGCGGTCTTCAGGGCGTCGGCTATC +TCTCCCGGCTTCTCGACCAGCATTCCTCTGGCCCCGTAGGCCTCGGCTATCTTGGAGAAGTCCGGGTCGGCGCCAAGCTCGGTCTCGCTGTACCTCTTGT +TCCAGAACAGCTTCTGCCACTGTTTGACCATTCCCAGCCATCCGTTGTTCAGCAGGACTATGACGACCGGCAGGTCCTCGGCCACCGAGGTGGCCAGCTC +CTGTTGGACCATCTGGAATCCCCCGTCCCCTGTTATGGTCAGGACGGTGCTGTCGGGCTTGGCGGCCTTCGCCCCTATGGCGGAGGGGAGCCCGAAACCC +ATCGTGCCGAAGCTTCCCGAGGAGAGGAGCTGTCTGGGCCTGTGGACGTGCAGATGGTGCATGGCCCACATTTGGTTCTGTCCCACGTCGGTGGTGACTA +TCATGTCGTCGTCCTTGTCGATCAGCCTGTTGATCTCGTATATGACCTTCTGAGGGACGATCGGTGTAAGGTCTATGTCGATCTTGCACCTGCAACGCCT +CCTGTACTCCGCATAGGTGCTGTTCCAGTCGGCATGGGTATCCCTGTATCCGGAGAGCCCGTCGATGAGCGCCGCGGTACCCTTCTTAGCATCGCAGAGA +AGGTTGACGTCGTTGTTCTTGTGCTTGTCGAACTCCGTCGCGTCTATGTCTATCTGGACGACCCTGCATGCGCCGTCGAACCTGGTGTGGGGGCTGAACG +TCCTGTCCGAGAACTTCGTGCCTATGGCTATTACCAGGTCGGCGTTGCGGAAAGTATCGAGGGCGCACATCTTGCCGTGCATCCCCAAGGGGCCCAGGCT +GAGCGGGTGCTCGGTGGACATGGCACCCAATCCCATGAGCGTGAAGACCGCCGGCGCGCCGATGAGCTCTGCGAGCCTCGTAACTTCCTCGGACGCGTTC +GCGCTTATCGTTCCGCCGCCGATCAGCAGGACGGGCCTCTGCGCTTCCTTGATCCATTGGACCGCGGTGCCCAGTTCGGACATGTCCTCCCTGGGCTCCT +TGATCCCGTACGAGATGCCCAGGAGGCTCTCGTCGATCTCCGAGTTCATCTGGTCTGAGGGGAGGTCGATGTGGACAGGCCCCGGTCGCCCGGTCTGGCA +CATCTTCCATGCCTCGTCCACCGCATGGGGCAGCCTGTTGACGTCTAGGACCCTGAAGTTGTGCTTCGTTATAGGCATGAGGAGGCTGTACGCGTCCACT +TCCTGGAAAGCGCCGAGCCCCAGGGACCCGGTTCCGACCTGTCCGGTAAGTGCCAGCATGGGAGTTGAGTCCGCATACGCCGTGCCTATGCCGGTGATCA +TGTTGGTGGCACCGGGCCCGCTGGTGGCCATGCAGACGCCCGGCCTCCCGCTGGCCCTGGCATATCCGTCTGCCATGTGGGCGGCGCACTGCTCGTGGCG +TACTAGGACATGGTTTATCGATGAGTTCATTATCTCGTCGTAGATCGAGATTACGCTTCCGCCCGGATATCCGAACATGGTCTCGACACCTCTGTCCTCC +AGCATTTGGAGCAATGCTCTGTTTCCTTTCATGGTTGGTCTCCGGCGACGTATCGCGCTTGTTTTTTATAATTCTATTTGGAAAAGCGCGCCGAAACGCG +CCAGCGGAAGAAGTTTATGTATACGGGGGCCATATGCCCACGCAGGTGTTTCATGGCTGTAATAAAGGTCGGTATCAACGGATTCGGAACCATAGGGAAA +AGGGTCGCCTCCGCAGTGAGCGCACAGGATGACATGGAAGTCGTAGGTGTGACGAAGACCCGCCCGTCCTTCGAGTCGGAGGTCGCAAGGTACAGGGGAT +TCGACCTGTACGCGCCTCAGAAAAGCGTCGAACTGTTCGACAAAGCGAACGTGCCGGTCGGGGGGACCGTCGAAGACCTCTGCGGCAAGGTAGACATCAT +GGTCGACTGCACGCCCGGAAACGTAGGGCAGGAATACAAGGCGATGTACGCCAAAGCAGGCATAAAGGCGATATTCCAGGGAGGGGAGGACCACAGCCTG +ACGGGGATATCCTTCAACTCCACCGCCAACTACAAGGAGTCCTGGGGCGCCCAGTTCTCCCGTGTCGTTTCTTGCAACACCACGGGGCTGCTGAGGACGC +TCTACCCCATAGACCGCGAGTTCGGTATCGAGAAGGCGTACGTAACGTTGGTCAGAAGGGCCGCGGACCCCGGTGACAGCAAGAACGGGCCGATCAACGG +GCTGGAGCCCACCGTCAAGCTGCCGACCCACCACGGGCCGGACGTCCAGAGCATCATGCCATGGGTCAACATCAACACCATGGCGATAAAGGCCTCCACT +ACGTTGATGCACATGCACACGGTCACGCTGGAGCTGAAGAACTCCGCTTCCACCGAGGCCGCGGTCGAAGCGATAAGGAACTCCTCGCGCGTCAGGATGG +TGGACGCGGCGTCCGGCATCAGGTCCACGGCGGAGGTCATGGAGCTGTCGAGGGACCTGGCCAGGGACAGGTCCGACATGTACGAGATCGTGGTATGGGA + +>contig_38063 +CTATCTCCTCAGGAGGTCTGGGAATCTCTGATCGGGAAGAACAGTAACTACCGCATCATAGTCGTGGACCTCAATCTGACCCGTGTGCTGTTCGGCATGA +TAGTGGGCGCCGGCCTGGCGGTGGCCGGTGCGGTCATGCAGGCCCTGTTCAAGAACCCGATGGCCTCGCCTTATACTCTCGGGCTCTCGTCAGGCGCCGC +ATTGGGCGCCGCATTGGGGATTCTCTTCCCTCTTTCGTTCGTACCTGAGGTCGCATCGGTCCCAATCCTGGCTTTCGTTTTCTGTCTGGGGACCATGTTC +CTCGTGTACTCTATTGCCAGAGTGGGCAACCAGACGCACATGGAGACTCTTCTGCTGGCCGGAATAGCCGTAGCGGCATTGGCGCAGGCGGCGGTCTCCC +TGCTCACGTACATAGCGGGCGAGAGCATCACGGAGATAGTCTTCTGGGGAATGGGCAGCCTGACCGTCAGCCTCCCATGGGTCAAGATCCCGATAGTGCT +GGTCCTCAGCGCCGTGGGCATATTCGCAATGCTCTACTACGCCAAGGACCTGAACGCCATGATGCTGGGGGACGCCCACGCCATGGACCTTGGAATAGAC +GTAAAAAAGACAAGGCTGGCACTGTTGATCGCCTCGTCTCTCGTCACCGCGGCTGCGGTATGTTTCGTGGGGACCATCGGCTTCGTAGGCCTTGTGATCC +CGCACATACTCAGGATACTTCTTGGTCCGGACAACCGTCTGCTTCTGCCGATGTGCGTGCTGACCGGAGGGATATATCTTGTAGGATGCGACTATCTGGC +ACATCTCTTCGCCCAATCTCTGGGCGTCATGCCCATAGGCATAGTGACATCTCTGATAGGCGCCCCGTATTTCATCTATCTGCTCAGGAGAAGAAAAAAG +GAGGTGGGATGGGTATGAGCCTGGATATCCGTGACTTATTCTACAATTACGATGGGAAGCCTGTTCTCAAAGACGTTTCGTTCCTGGTCAAGGAAGGAGA +GGTCCTGGGGATACTGGGGCCCAACGGATGCGGAAAGACGACCCTGCTGGGCAATCTGAACAGGAATCTGAGCCCCAAAGGCGGATGCGTGCTTCTGGAC +GGGGAGGACCTTCACAATTACAAGAAAAAAGACATCGCGAAGGAGATAGCGGTGGTTCCGCAGGACAGTCGCGTAGGTTTCTCGTTCACCGTAAGAGAGA +TCGTCTCCATGGGCAGGATGCCATTCCAGGACGCCTTCCAGGGAGACTCCTCGGAAGACCTCAGGATAATCGAAGACGCGATGAGGAAGACCAACGTACT +GGATATGGCAGACCGTTACGTGAACACCATGAGCGGCGGGGAAAGGCAGAAGGTCATAATCGCCAGGGCCATGGCGCAGACGCCCAAGATACTGCTGATG +GACGAGCCC + +>contig_44250 +GGTGATGTACTGGGGCTTGTAGGCTACTTTGACCTTTGCGTCTATCTTGCCGCCGTCTGGAGGGATCTCTCCGGCCAGCATCTTTACGAAAGTGGTCTTT +CCTGTGGCGTTGGGACCGACGACCCCGACGGATTCCCCCATCTTTATGGAACCGCCGACGACATCCAAAGTGAACTCTCCGAAGTCCTTGGACAGGCCCT +CGAAGGAAAGCAGGTCGGAAGTGACCCAGTCGCTCCTGGGAGGAGACGCGAAGAACTCTATCGGCCTATCCCTGAAACGGATATTCTCTTCGGGAAGGTA +ACCGTCCAGATATACGTTTATGGCGGTCCTGACCTGTCTTGCAAGAGTGAACACGCCGTACGCCCCCTCGGTACCGTATACAACGCTGACGATGTCGGCG +AGGAAATCGAGTATGGCAAGATCGTGTTCTATCACGACCACCTGCTTTTCTGCGCTGAGTTCTTTGATGATGCGTGCCATCCTGATCCTCTGGTAGATGT +CAAGGTACGAGGTGGGCTCGTCGAAGAAGTATACGTCCGCGTCCTTCATGACCGTGGCAGCCATGGCGACCCTCTGAAGCTCTCCTCCTGAAAGTTTCTT +TATATCCCTGTCCAGAAGCTCGGTCAGCTCGAACATGATGGCGGCCTCCTCGAGTGTCAGGCGGCCTTTTATGCCGGAAAGCAGGTCCTTCACGGGCCCC +GATGCGGCTTTGGGTATGAGGTCCACGTACTGTGGCTTTATGGCCGTCCTCACCTTGCCGGCGTAGACGTCCGTGAGATAGGATTTGACCTCGGTACCGT +CGTAGTGCTGCAGCACTTCCTCTTTGGATGGAGGTTTCTCATAGTTGCCCAGGTTGGGGACGAGTTCCCCGGAAAGTATCTTGATCGCCGTGGATTTTCC +GATCCCGTTCGGTCCAAGTATGCCCGTGACCATGCCTTTCTTCGGCACCGGGAGCCTATAGAGGCGGAAGGCGTTCTCGCCGTACTGGTGGACCATCTCC +GTCTTCAGCTCGTCGGCCAGGCCTATGATCTTTATGGCGTCGAACTGGCATTTGTTGACGCATATCCCGCATCCCTGGCACAGGGATTCGGATATGATGG +GCTTGCCCCTCTCGCCGAACACTATGCATTCCACGCCCGTTCTGACCAACGGGCAGAACTTATAGCATTCCTTGTTGCATTTTCTGTTCTGGCATCTGTC +CTGCAGGACGGCCGCAATACGCATGTCCCCGCTTAGACCGATTTAAGATATAACCTTTAAGGATGGTATCGCAGATAAGCTGATAAGGGAAGACGGAGAC +AGATGGGCATGGCCGAAGCGGATGGGACCACCGAGGACGTCAGGATACTTACGGGCGACTACAGGAGGGCGATAAGGCATCTCTCCATACCGATAGCCGT +GGCTCTTGCGATACAGCATATCAACATACTCGTAGACACGTTCTGGGTCGCGGGCCTGGGGGCGGACCCGATGGCTTCAATAAGCATAGTATACCCGGTT +TTCGCCACGGTCATGGGCATCGGAAGCGGGCTGGGGATCGGTGCTTCTTCCGCGATAGCCAGAAGCATCGGGCATAACAGGAGGAAGGAAGCCGGCACGA diff -r 000000000000 -r 11a61934bfb3 test-data/genome2.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome2.fna Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,51 @@ +>contig_11394 +GCTTTTTACGCCCAACGGGCTTGTTCTTGCTCAGACAGTCCAAGGCTTTCCAGATATGATAATCGCTGAATTTCGGTATCGGGCCGCCTGCACCCCTGTG +CTGCTGATTGGACATATGGATGTATCATTCATCCATTAAATAAAGTAATTGATTGTCATGTCGCAAGATACGGTATTAACGCCGTCAATAGCTGTTAAGC +CAGTGCCCGCCGTCGCTTTCCATCCGTAATACTCGCGCGTTTTTTATATCGAAGGAACTCTTCACATCCATGGTTCAAAAGTCGGTGGACTTTGTTATTA +TTGAGAATGTTTCCAAGAGGTTCGGGAACAAGACGGTCCTTAATAATGTGAGCGCCACTATACAGACCGGTAAGATACTGGGCCTGATAGGCAAGAGCGC +CGCGGGCAAGAGCGTTTTGATAATGATGCTGAGGGGAAGCGAAGATTACGCACCCGACTCCGGAAGGGTGCTGTACAGGGTCAATAGGTGTTCCGGATGC +GGAAACCTCGACCTCCCCCATGAAGGAACGCCCTGCTCGAAATGCGGGTGTGAAACAGGAACGATCACCGTGGATTTCTGGTCTTTGAAAGATGACGACC +CTTTAAGACGCCAGCTCAAGAGCCGCATCGCCATAATGCTGCAGAGGACGTTCGCCCTTTTCGGGGATAAGACCGTGATCGAGAACATCTTCGAGGCCAT +AGGCGACCGTGCAGAGGGCAAGGCCAGGACGGACATGGCGCTCCAGCTGCTGGAATTCGTGGGGATGACTCACAGGACCACACACATAGCCAGGGACCTG +TCCGGAGGAGAGAAGCAGAGGATAGTCCTCGCAAGGCAGATAGCCAGGGATCCTCTCTTCTTCTTGGCGGACGAGCCGACGGGAACGCTTGACCCGTACA +CGGCGGAATTGATGCACGAGCGTCTTGTGGACTACGTCGGGAAGAGAGGGATCTCGATGGTCTTCGCGTCCCATTGGCCCGAGGCCGTGGATAAGATGGC +CGACGAGGCCATATGGCTGGATTCCGGCAACGTGCTGATGCAGGGCGACCCGAAGGAGATCGCCGATAAATTTATGGAAGGATACTCGTTCGAAAGGACA +AAGGCCGCCGACCTGGGAGAGCCGATAATATCGCTCAAGGATGCGGAGAAGCACTTTTTCTCTGTCGTCAGAGGAGTCGTCAAGGCAGTGGACGGTGTAA +CCTTCGATATAATGGAGCGCGAGGTGTTCGGCCTTGTGGGAAAGTCGGGCGCCGGCAAGACCACGACGTCAAGAATGGTCGCCGGCATGACGCCCGCCAC +CCGCGGGTCCGTGAAGATAAGGATCGGCGACGACTGGGTTGATATGTCAGAGATGGGGCCGAGCGGGAAAGGCCGCGCCACCCCCTATATCGGGTTCCTC +CATCAGGAATACACGCTCTATCCCTTCGACAACATACTCAGCAACCTTACGACCAGCATAGGCACCAGGATGCCAGCGGAACTTGCAAAGTTCAAGGCCA +TACAAGTGCTTCAGAGCGTAGGGTTCGACAAGAAGAACATGGAGAGTCTTCTCTACTCTTACCCCGACACACTGAGCGTCGGAGAGTGCCAGAGGATAGC +CTTCGCACAGGTCCTGATAAGGGAGCCCCGCATCATAGTGCTGGATGAGCCTACAGGGACAATGGACCCGATAACAAAGACCATCATAGCAAAATCCGTC +ATCCGGGCGAGGGAGACCCTGGGCGAGACCTTCGTCGTGGTGAGCCACGACATGGATTTTGTCGAGAACGTCTGCGACCGCGTAGCGTTCATAAGGAACG +GCGTCGTGGAAGACATGGGAACTCCCGAGTCGGTCATCCAGAGGTTCGGTCTGAAAGAGCTTCAGGATGACGACTCCGAGGGTGAATGAATGAAGCAGCA +GATCGGGCGCCACCTCAGCTTCGTTGAATGCAGAGAGGCCATGGGGCTCGGCGTGGGCGGTGCCCTGGCACAGAGGGCGACCATCTCTGACAGCGGAAGG +GACGTCGTTGCGGTGGCCATGGGCCCGGGCAAGAGGCACATAACCAAACCGGTATGCGAGATAACATATGCCCTCAGAGAAGAGGGCATAGATACCAGCG +TCGCCTGAGCGCCTGGCACTTATTGCGGAGTATGTCAAGGACATGATGACCGAACTCGAACCGGACAACGCGGCCGTCTTCGAAGCGGGATGCGCCAGCT +ACCGGGCCAAGGTAGATGTGCTGATAGGGCTTGAACAAGAATATCTGACAGGCAAGGCGACTACCGAGATCATCGTCTGGCACCCTTCCTGGGCGTATCT +TCTTCCGGATAATGTGACCGAGGCAGAGCTCATGGAAGCAGCCGAGGCGGCATCCACGCCCTCATCGATCGCGATGCTGCAGGGAGGGACGCCGGAAAAT +CCTATCAACGTGTTCCTTTCGGAACCCGAAGAGATCAACGGTCTTACCCAGCAGGGGCTTTGTGAAATGGGAATATATGTAAACATAATAGTGATTAACA +TACTCGCCGGGGACTGGGTCGAATATCTGGGCCAGGTCATCGAGATACTGGGAGATAATATTCCGGATGCGGGGACATGAATTGATGATACCAATAGAAA +TTAAGGACCTTACCGCTGGATATGACGGCCGAGCCGTTTTCAGCAACGTCGACCTGGAGCTCAGGGACAAAGACTTCCTGGCGGTCATAGGGCCCAACGG +CGGCGGGAAGACAACGCTCTTCAGGGCGATCCTGGGCCTAATAAAACCCATGGGGGGGACCGTAAAAGTGTTCGGCAAGGAGCCGGCAGGTTCGCCCCCG +GGCATAGGATACGTTCCGCAGAACGAGAATCTGGACTCAGAATATCCAATAAGTGCCAGGGAAGTCGTCCTTATGGGAATGAGGTGCAAGAAGGGCCTTA +GGCCGTTCTATTCCAGTGAGGAGAAGGAGTCCGCAGAGAGGGCCATGGAGTACGCCGAGGTCTCGGATTTCGCAGACAGCCGAATAAGCAACCTGTCGGG +AGGGCAGAGACAGAGAGTATACCTCGCAAGGGCTCTTGCCCCGGAACCGAAGATACTCATGCTGGACGAACCCACCGCGAGCCTGGACCCGTCGATGAAG +GACTGCACCTACGACATACTCAGGAAGCTGAACAGGGACGGGATAGCCATAATGGTGATAACTCACGATATGAGCAGCATCTCTCATGATGTCAAACGTG +TAGCATGCATGAACCGCAGGCTGATAGTCAACGATGCGCCCGAGATAACCCAGGAGATGATCGCATTGGGATTCCACTGCATCCCCGAGCTAGTGCACAT +AGGTCCCTGCGATTGCGGAGGTCACAACGATGGTTGATTGGGTCGCGGCATTCTCGATGCCTCTGATTCAGAACATGTTCATGGTCGCGGCCATAGCATG +CGTTCTTTGCGGAGTCGTGGGAACCCTGGTGGTCGTGAAACGGATGGTGTTCGTAACGGGTGGCATAGCACACACCACTTTCGGAGGTGTGGGTCTTGCA +TATTATGTTATGTCCGTCGTCGCAGTCTCATGGTTCACCCCCATGATCGGCGCCGCACTGTTCGCGGTCGTTTCGGCGGTCATAATGGCGCTTCCCGCGG + +>contig_159 +TATAGCTCAGCTCGTTGGCGGAGACGCTGCTTCCGTACATCTGGCCGCCGCCGTTGATGCCGCCGCCCCAGGCGGCCGTCCCGATCCCCACGGGAGAAAT +GTCCGTACCTCGGAACCTTATGTTTCTCACGGATTCCCGTATATGTTCCTGGATTATAACTGATACGCAATCCTGTTTCCGACGTCCGCCATGTTTAGAT +AAATTGACGGTATAGCCGAAGGCATGGATATGGCAATGGAGCTGAGGAACGTCTCCGTAGTGAGGGACGGGAAGCGGATACTGGATTCCGTCTGCCTCGA +TATCGGCGCCTCCGAGAACGTTGCCGTCATAGGGCCGAACGGTTCGGGGAAGACGACGCTCATCAAACTGCTGAGGGGCGATATTTATCCCTACTACGAC +GAGGACCGCCCCGCGGAGATGAGGATCTTCGGTGAGAAGATATGGTCCATCTACGACATACGGAGCCGCATGGGCGTGGTCTCCATGGACCTCCAGGGCA +TGTTCGGCGGCGAAACGCTGGTCGGAGACGTCATAATGTCGGGATACTTCAGCAGCCTGGACATTTTCCGCAACCATGAGGTCACCGACAACATGCGCTC +CGGGGCCTCGCGAGCGGCCGGGTACATGGGAGTGGAACATCTCGTCGGCAGAGATCTGTCCGGCCTTTCTCTGGGAGAGATGAGGCGGACGCTGATCGCC +CGGGCGCTGGTCACCGCCCCCGAGATGCTCGTCCTCGACGAACCGATGACGGGCCTCGATATTGTAATGAAATCCAAATTCAGGAAGATGTTCGACATCA +TGACGGAAACGGGAGTGAGCATCGTCATGATAACCCACGACCTCACCGACATCCCCGTTTCCTTGAACCGCATAATAATGATCAAGGATGGGAAAGTGTT +CGCGGACGGTCCTAAAAAAGACGTCCTGACGTCCGAGGTCGTCAGCGGGCTTTTCGATGAACCTATTAATGTACAATGCGTTAACGGGATATATTCAATG +AGGATGGATGAGTGACAAGGTATATCTGTTCCGAATGCGGGAACGAGATTCCGTACGTTTCGGATTTCTGCTACCAGTGCGGTAGCCTGAAGAGCAAGGC +GTTCAAGATAGACGAGGGCGGCGAGATGGAGGGCGGGGAGGTCCCGTGCCCCAACTGCGGAAAGCCCATAGAGGAGGACGCCCGGTACTGCAGGCACTGC diff -r 000000000000 -r 11a61934bfb3 test-data/genome3.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome3.fna Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,60 @@ +>contig_4003 +ATCAAAGAGGAACTGAAGGCGGCGATGCTGCTGACCGGTTCCTCTGACATAAGAGAGCTCTCTGATGCAGAGTATATCGTCATGGGAGAGACACGCAAAT +GGATGGAAGGCCTGAAATGACCGACGTCAAGAAGATATTGAAACAGATGTCCGACGAGCTGAGCAAGCCGATCGAATCATACATAGAAGACGAACTGCCC +GCCAATCTCATCGAAGCGGCAAGACAGTACCCCTATGCCGGCGGAAAGAGGATGAGACCGGCCATGGTCATCGCCGCGTGCAGGGCGGTGGGAGGGGATG +GCAGGAAGGCCGTTCCCCTTGCGGTTGCCATAGAGTACATACACAATTTCACGCTGATCCATGATGACCTCATGGACGGGGACGAGAAGNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCATGGACGGGGACGAGAAGCGCC +GGGGCATGACCACATCCCATGTGAAGTACGGCATGCCCACAGCGGTGTTGGCGGGAGATGCCCTGTTCGCTAAGGCCTTCCAGATAATCGCCGACCTCGA +TGCGGACGGCGAAACGGTCAGAGATGTCCTTAGAGTGGTCTCCCAATCCGTCTGGGACCTGGCCAGAGGTCAGCAGATGGATATAAACAACGAGAACGGG +ACCGAGGTCACCATGGATGAGTACATCGAGACCATCAGACTGAAGACCAGCGTTCTGTTCGCCGCCGGTGCCGCCGGAGGCGCTATGATCGGAGGTGCGA +GCAAGGAGGTCGTGGACGCCGTCCACGGCTACGCCATGAACCTGGGCGTCGCCTTCCAGATGTATGACGATATACTTGGGATAGTCGGGGACCCGGCCGT +TACCGGTAAATCGTCCGGTAATGACATTCGCAAAGGGAAGAGCACCGTCATCGTGTGCCACGCCCTGAAGAACATAGCTGACAGGGCGGACCTGCTGGTC +TTCCGCGATATCCTCGGCAAGACAGACGCCACCGATGCGGAGATAGACGAGGTCAGGAGCATACTCCGAAGAGCCTGCAGCCTGGATTACGCCATAGAGA +CCGCAGAGGATTACATCAACAAAGCCGTCGACTGCCTGGATGCGCTGGAGCCCTCAAAGGACAAGGACTTCATGATAGCCCTGGCAGAATACACGATGAC +CAGGACCCTTTAGTCGGAGATCCCCTTCTCCGTTATGGAGTATGTGGCTTTCCGGCCTTCCGGTATGCTGCGGTGCTTGACCATGATCGCGGCCCTGCGG +CCGTTGCCTTTCTTCTCCAAGCGGATTATGGTCTTCGCGTTATGATGCATGGCGTGGCCTCCGAGGAACTCTATCGTACCGGCGCCTATGTTGGTGTATA + +>contig_4403 +CACCGGTCACCCGAAGGTCACGCGCGTATCGATGCGTGACATCGCAGACCTGGGAGAGAGGGGCCTGTACATCCTTCACGAGATCGGTACGGACCTCGTC +GGCAAGATGGAGGGCTGCACCGGGTGCAAGAAGTGCGAGCACGAATGCCCCGAGAACGCGTTGACCGTAAGCAAGGACAAGACGATCACCGTGAAGACCA +AGAACTGCCTCGGAACGGCATGCTACAGATGCCAGTACGTCTGTCCCGAGAAGGTCATGCAGTTCGACTCCCTAAGGCTGTCGTGATAAACGGTTTTGGG +CGGGGCCGGCCCCGCCCTTTTTTCATTTACCGCCGTTCAGGGCCTCGGCGTGCACGGCAGGCCTGACATTCTCGTCCTCCAGCTCCGTAAGTATCTGCTT +GCGCAGCCTGATGAACTCGGGCGAAGCGCGGTCCCTGGGCCGCGGAATGCCTATGTCCACGATGTCCTTGATGCTGGCAGGACGCTTGGTAAGGACGACT +ATCCTGTCTGAAAGATAAACGGCCTCGTCGACCGAGTGGGTCACGAACAGGATCGTAGTGTCCGTCTTCTCGACTATCCTCAGCAGCTCGCCCTGCATGA +TGTTGCGCGTCTGGGCGTCCAACGCGCCGAACGGCTCGTCCATGAGCAGCACGTCGGGCTTGGTAACAAGGGCCCTTGCGATGCCCACGCGCTGCTTCAT +ACCTCCGCTGAGCTCGTGGACACGATGGTCCTCGAAACCTTCGAGGCCGACCGCCCTGATGTAGCGTTCGGCGGTCTTCCTGCGCTGCTCCGCCGGGACG +CCGGCGATCTCCAGGCCGAACTCGACATTCTTCCTTACAGAACGCCAAGGGAACAGTGCGAACTCCTGGAACACCATGCCTCTGTCGGGGCCTGGCCCGG +TGCACTTCTTCCCGCCTATCGACACTTCTCCGGAGGACGGCTCCATGAGCCCTGCTATAAGCCTGAGCAGAGTCGTCTTTCCGCATCCCGAGGGACCGAC +TATGGATATAAGCTCGCCCTTCTGGATCTCCAGAGAGAAATCCTCCAGGGCCACGGTCTCCTGTTCATCGGTCTTGTAGACCTTCCTCAGATGATTGATA +ACGATCTTCTCGCTCATTCTATCCCCATCCTTCTTGTTATGACCTTGTGCAGATAGTCGGCGAGGCTGGTCGTCAGTATTCCGAGGATTGCGATTATGAC +TATGCCCGCGTAGACGTTGGGCCAGTACCCCATCTGCGCCTGTATGCTGATGAAGTATCCGACGCCTCCTCCGAACGATGCGTACAGCTCGGAGGCAACT +ATGCACATCCACCCGACCCCCATGCCTATGCGGAGGCCGTTCATTATGTATGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN + +>contig_14302 +GATGTGGAATGCGGCCAAATGCCGCCTCGGTTTCAGCGGGGCAAGGCGTTCCATGTCCACGACCGCTGGAATACTGGTGAACGTTTTCATTACTTCTCTG +GAGATAGCCGAACGTTCTCAGCCTGCGCTCGAAAGCAGGAACTACAACGGCAGTTTCCCCATTTATAGGATGCCCAACAAGATCGGTCTCTACTGGTTCG +CCATCACGGCCGCCGCGTGCGCCTCGCTATACATCATCGGATACTACATCTCGACCCCGAACATGGCGGCAATACTCCTGGGGGCGGTCTGACGGTCTGC +GACCTTCGTACGGATAAAGTGAGCTACAGGTACGGCAATTCGAATTACAATGCTATCGATTCTGTGGATTTCACAGCCTCCCATGGCAGAAGGACCGTCA +TCCTGGGAGAGAACGGGTGCGGCAAGTCGACGCTGATATATCAGCTCAACGGAGTATACAAGCCTGTTTCCGGTACTGTGTTCTATGGAGATATGCCCAT +ATCATACGACAAGGAGTTCCTTACGGAGCTGCGTTCCGACGTTTCCGTTGTTCTGCAGAATCCAGACGATCAGATTTTCTCTTCCACCGTCGAGGAGGAC +GTGGCATTTGGACCGTTAAACTTGGGCCTTTCCCGGGAAGAGGTTGGAGAAAGAATCGGCCGGTCTTTGGAATGCGTGGGGATGTCGGGATTTGCCGAAG +TGCCTGTTCAGCGCCTTTCATACGGTCAGAAAAAAAGAGTGTCACTCGCAGGCGCCCTAGCATCACATCCAAAGATACTGGTCCTGGACGAGCCTACCGC +AGGCCTGGACCCGCAGATGTCCAGAGAGGTGATGGAGATCGCAAATTCTCTCATCAGAGAAGGGATCTCCGTCGTAGTATCCACCCATGACGTGAATCTG +ATCTACAATTGGGTCGAGGACCTTTACGTGATGCGGAACGGACACATGGTCTTCTCCGGAGATGCGGACGAGTTCTTCTCCGACCGTCCGTCCGTTTATC +TTTCAGGTCTGGAACAGCCCTCGATATTCAGCATAAACCACAATATGGAGACGTTAAGAGGGACGATTCCCGCGTCATATCCCAAGACCATGAGCCAGAT +GGTCAGCAGATTATTCCCTTCAGGATCCTCGGCCGGAAGGATATTCATCTATCAGACTGAAGGCGAGCGCATCGACCAGGATGCGATCGAGGAGGCCGTG +GGAAAGAAAGGGATGCCCATTGCAGTATACGGCCCCTCCGCGCGCAGGTCGGTGACCCGATCGAAGCTCAGGGTTGATTTCTATTTTAACGGCATAGAGT +GTTGCATCAGGGAGGCCATGGTAAACCATGATTCCCTGATAATAGTCGACCGGGGCTTGAAGGGGATCGTCACGGAGGCGATTGAAGAGCTTAGGGCATA +CGGAACCCGGATCAGTATCAGGGAGTTGGTTTTTTGAGCGCTCCCCTTTTCCGCACCGAAGGTCTTTTCTTCAGATACGAAGGCGGCCGGGGGGACGCGT +TGGCAGACGTGAACATCACGATCAAAGAGGGTGCCAGAACTGTCATCATGGGAGCCAACGGAGCTGGAAAATCCACGTTCTTCTATCATCTTAACGGAGT +CTTGAGGCCGTCGAAGGGCTCGGTGTTTTTCCGGGGAGAAAAAATACCGCACAGGGGAAAAGCTCTCAGGAAGCTGCGCTCGGAGGTCGCGGTGATGCTC +CAAGACCCCAACGACCAGCTTTTTGCACCAAAAGTATCTGACGACATAGCATTCGGCCCGAAGAACCTGGGACTCGACGCTCAGACTGTAGGGGAGAGGG +TCAGGGACGCCCTCTACATCACAGGCATCGAATCTCTGGAGGGTCGCAGCGTGATGCAGCTGTCGTTCGGCCAGAAGAAGAGGGTGGTGCTGGCCGGTGC +CTTGGCGATGCATCCGAAGGTGCTTATAATGGACGAGCCCACCGCAGGTCTCGATCCCCAGATGTCCAAGGAGCTCATCGAGCTCGCGGACGAGCTGCAC +CATCTTGGAACGACCGTTATTTTTTCAACCCATGACGTGGACCTCTCATATTCTTGGGCGGACGAGGTCCATGTCCTAAGAGGGGGCCGTAATGTATATT +CGGGGAGCTCAGAAAGATTCTATGACGATACTTCGGAAGTTTATCTTTCGGGCCTTGTCGAACCGGCCATGTACGACATCAACGTCAGCATCTCCGAGCT +TGCCGGATGCCCCGTTGAACCGTTTCCCAAAACCCTGCCTCAGCTTGTGGCCAAGGCAGTGCCGTCAGAGGGGCCGGGCACGGTTCACATCCTTCCCGTG +GAAGGTCCGGTCGACCGGGAGCTGTTCTCCTCTCTGACGTCCGGGTCCGGGATGTCCGCAACAGGCGTCTACGGTACTAATGCAAGAAAATCTGCGGAGG +CTTCCAAATTGCCGATAGATTATTTCTTCGGGGCCGACGAGGGATGCATAATAGAGGCTTTGCACGGCAAAGACACGCTGATATGCTGCGACAGGTCCCT +TACAGATCTGCTGATATCGAAGATAGGCAGTATGTCCCGGTTCGGGACAGAGGTCCCTTATTCTCTGCACTGAACATTTCTTTTTTCCGGGGGTTCGAAC diff -r 000000000000 -r 11a61934bfb3 test-data/test_contig.contig2classification.names.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_contig.contig2classification.names.txt Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,4 @@ +# contig classification reason lineage lineage scores superkingdom phylum class order family genus species +contig_38063 classified based on 1/2 ORFs 1;131567;2;1783272;1239;91061;1385;186820;1637;1639 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Firmicutes: 1.00 Bacilli: 1.00 Bacillales: 1.00 Listeriaceae: 1.00 Listeria: 1.00 Listeria monocytogenes: 1.00 +contig_44250 classified based on 1/2 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Proteobacteria: 1.00 Gammaproteobacteria: 1.00 Vibrionales: 1.00 Vibrionaceae: 1.00 Vibrio: 1.00 Vibrio cholerae: 1.00 +contig_9952 classified based on 1/5 ORFs 1;131567;2;1783272;1239;91061* 1.00;1.00;1.00;1.00;1.00;1.00 Bacteria: 1.00 Firmicutes: 1.00 Bacilli*: 1.00 not classified not classified not classified not classified diff -r 000000000000 -r 11a61934bfb3 test-data/test_contig.contig2classification.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_contig.contig2classification.txt Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,4 @@ +# contig classification reason lineage lineage scores +contig_38063 classified based on 1/2 ORFs 1;131567;2;1783272;1239;91061;1385;186820;1637;1639 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +contig_44250 classified based on 1/2 ORFs 1;131567;2;1224;1236;135623;641;662;666 1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00;1.00 +contig_9952 classified based on 1/5 ORFs 1;131567;2;1783272;1239;91061* 1.00;1.00;1.00;1.00;1.00;1.00 diff -r 000000000000 -r 11a61934bfb3 tool-data/cat_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/cat_database.loc.sample Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,7 @@ +## A typical download from https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190719.tar.gz +# ls CAT_prepare_20190719/ +# 2019-07-19.CAT_prepare.fresh.log +# 2019-07-19_CAT_database +# 2019-07-19_taxonomy +#value name database_folder taxonomy_folder +#2019-07-19_CAT_database 2019-07-19_CAT_database /opt/galaxy/tool-data/cat_database/CAT_prepare_20190719/2019-07-19_CAT_database /opt/galaxy/tool-data/cat_database/CAT_prepare_20190719/2019-07-19_taxonomy diff -r 000000000000 -r 11a61934bfb3 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,7 @@ + + + + value, name, database_folder, taxonomy_folder + +
+
diff -r 000000000000 -r 11a61934bfb3 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Dec 10 16:05:34 2019 -0500 @@ -0,0 +1,7 @@ + + + + value, name, database_folder, taxonomy_folder + +
+