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phnmnl / container-galaxy-k8s-runtime

PhenoMeNal runtime for Galaxy running inside a container orchestrator
Apache License 2.0
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Fix missing tab separators in isa_cvterms #212

Closed ilveroluca closed 6 years ago

ilveroluca commented 6 years ago

I found galaxy complaining about some of the entries in the isa_cvterms table:

galaxy.tools.data WARNING 2018-06-20 17:40:14,696 Line 425 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
402 Hommel false discovery rate correction (STATO:000542)       statistics
galaxy.tools.data WARNING 2018-06-20 17:40:14,696 Line 426 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
403 Student's t-test (OBI:0000739)      statistics
galaxy.tools.data WARNING 2018-06-20 17:40:14,696 Line 427 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
404 Wilcoxon rank sum test (STATO:0000076)      statistics
galaxy.tools.data WARNING 2018-06-20 17:40:14,696 Line 428 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
405 Kruskal-Wallis test (STATO:0000094) statistics
galaxy.tools.data WARNING 2018-06-20 17:40:14,696 Line 429 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
406 Pearson's correlation coefficient (STATO:0000280)   statistics
galaxy.tools.data WARNING 2018-06-20 17:40:14,696 Line 430 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
407 Spearman's correlation coefficient (STATO:0000201)  statistics
galaxy.tools.data WARNING 2018-06-20 17:40:14,696 Line 431 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
408 Pareto scaling (OBI:0200037)        statistics
galaxy.tools.data WARNING 2018-06-20 17:40:14,696 Line 433 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
410 unit-variance scaling (OBI:0200149) statistics
galaxy.tools.data WARNING 2018-06-20 17:40:14,697 Line 434 in tool data table 'isa_cvterms' is invalid (HINT: '<TAB>' characters must be used to separate fields):
411 logarithmic transformation (OBI:0200094)    statistics
galaxy.tools.data DEBUG 2018-06-20 17:40:14,697 Loaded 408 lines from 'tool-data/isa_cvterms.loc' for 'isa_cvterms'
galaxy.tools.data DEBUG 2018-06-20 17:40:14,697 Loaded tool data table 'isa_cvterms' from file './config/tool_data_table_conf.xml'

This commit changes those spaces to tabs and so should fix the problem.