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annotate test-data/test-db/readme.txt @ 6:d4fbfd31696c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge commit 42b2d78b4badb653e84e15de35024368d48fce9b
author iuc
date Mon, 29 Jul 2024 07:03:15 +0000
parents 09b7b0b2e2c2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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1 *.dmp files are bcp-like dump from GenBank taxonomy database.
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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3 General information.
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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4 Field terminator is "\t|\t"
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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5 Row terminator is "\t|\n"
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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7 nodes.dmp file consists of taxonomy nodes. The description for each node includes the following
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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8 fields:
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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9 tax_id -- node id in GenBank taxonomy database
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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10 parent tax_id -- parent node id in GenBank taxonomy database
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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11 rank -- rank of this node (superkingdom, kingdom, ...)
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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12 embl code -- locus-name prefix; not unique
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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13 division id -- see division.dmp file
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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14 inherited div flag (1 or 0) -- 1 if node inherits division from parent
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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15 genetic code id -- see gencode.dmp file
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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16 inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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17 mitochondrial genetic code id -- see gencode.dmp file
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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18 inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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19 GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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20 hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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21 comments -- free-text comments and citations
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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22
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23 Taxonomy names file (names.dmp):
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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24 tax_id -- the id of node associated with this name
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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25 name_txt -- name itself
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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26 unique name -- the unique variant of this name if name not unique
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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27 name class -- (synonym, common name, ...)
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29 Divisions file (division.dmp):
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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30 division id -- taxonomy database division id
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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31 division cde -- GenBank division code (three characters)
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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32 division name -- e.g. BCT, PLN, VRT, MAM, PRI...
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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33 comments
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34
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35 Genetic codes file (gencode.dmp):
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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36 genetic code id -- GenBank genetic code id
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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37 abbreviation -- genetic code name abbreviation
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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38 name -- genetic code name
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39 cde -- translation table for this genetic code
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40 starts -- start codons for this genetic code
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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41
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42 Deleted nodes file (delnodes.dmp):
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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43 tax_id -- deleted node id
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44
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45 Merged nodes file (merged.dmp):
09b7b0b2e2c2 planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/recentrifuge commit fdcec50b71967011e4351eb347a9df2840be6bee
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46 old_tax_id -- id of nodes which has been merged
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47 new_tax_id -- id of nodes which is result of merging
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48
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49 Citations file (citations.dmp):
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50 cit_id -- the unique id of citation
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51 cit_key -- citation key
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52 pubmed_id -- unique id in PubMed database (0 if not in PubMed)
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53 medline_id -- unique id in MedLine database (0 if not in MedLine)
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54 url -- URL associated with citation
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55 text -- any text (usually article name and authors).
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56 -- The following characters are escaped in this text by a backslash:
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57 -- newline (appear as "\n"),
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58 -- tab character ("\t"),
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59 -- double quotes ('\"'),
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60 -- backslash character ("\\").
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61 taxid_list -- list of node ids separated by a single space