miga-base 0.7.24.0 → 0.7.26.0

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Files changed (295) hide show
  1. checksums.yaml +4 -4
  2. data/lib/miga/cli/action/add.rb +9 -6
  3. data/lib/miga/cli/action/derep_wf.rb +1 -1
  4. data/lib/miga/cli/action/index_wf.rb +4 -2
  5. data/lib/miga/cli/action/init.rb +83 -68
  6. data/lib/miga/cli/action/init/files_helper.rb +2 -1
  7. data/lib/miga/cli/action/option.rb +21 -2
  8. data/lib/miga/cli/action/preproc_wf.rb +7 -5
  9. data/lib/miga/cli/action/wf.rb +40 -24
  10. data/lib/miga/cli/base.rb +16 -5
  11. data/lib/miga/common/with_option.rb +1 -1
  12. data/lib/miga/dataset/result.rb +2 -1
  13. data/lib/miga/project/base.rb +1 -1
  14. data/lib/miga/result.rb +18 -15
  15. data/lib/miga/version.rb +2 -2
  16. data/scripts/essential_genes.bash +17 -1
  17. data/scripts/miga.bash +8 -2
  18. data/test/lair_test.rb +1 -2
  19. data/test/result_test.rb +22 -0
  20. data/utils/distance/base.rb +9 -0
  21. data/utils/distance/commands.rb +183 -81
  22. data/utils/distance/database.rb +68 -9
  23. data/utils/distance/pipeline.rb +14 -18
  24. data/utils/distance/runner.rb +17 -30
  25. data/utils/distance/temporal.rb +4 -2
  26. data/utils/distances.rb +2 -2
  27. data/utils/requirements.txt +5 -5
  28. metadata +5 -272
  29. data/utils/enveomics/Docs/recplot2.md +0 -244
  30. data/utils/enveomics/Examples/aai-matrix.bash +0 -66
  31. data/utils/enveomics/Examples/ani-matrix.bash +0 -66
  32. data/utils/enveomics/Examples/essential-phylogeny.bash +0 -105
  33. data/utils/enveomics/Examples/unus-genome-phylogeny.bash +0 -100
  34. data/utils/enveomics/LICENSE.txt +0 -73
  35. data/utils/enveomics/Makefile +0 -52
  36. data/utils/enveomics/Manifest/Tasks/aasubs.json +0 -103
  37. data/utils/enveomics/Manifest/Tasks/blasttab.json +0 -786
  38. data/utils/enveomics/Manifest/Tasks/distances.json +0 -161
  39. data/utils/enveomics/Manifest/Tasks/fasta.json +0 -766
  40. data/utils/enveomics/Manifest/Tasks/fastq.json +0 -243
  41. data/utils/enveomics/Manifest/Tasks/graphics.json +0 -126
  42. data/utils/enveomics/Manifest/Tasks/mapping.json +0 -67
  43. data/utils/enveomics/Manifest/Tasks/ogs.json +0 -382
  44. data/utils/enveomics/Manifest/Tasks/other.json +0 -829
  45. data/utils/enveomics/Manifest/Tasks/remote.json +0 -355
  46. data/utils/enveomics/Manifest/Tasks/sequence-identity.json +0 -501
  47. data/utils/enveomics/Manifest/Tasks/tables.json +0 -308
  48. data/utils/enveomics/Manifest/Tasks/trees.json +0 -68
  49. data/utils/enveomics/Manifest/Tasks/variants.json +0 -111
  50. data/utils/enveomics/Manifest/categories.json +0 -156
  51. data/utils/enveomics/Manifest/examples.json +0 -154
  52. data/utils/enveomics/Manifest/tasks.json +0 -4
  53. data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +0 -69
  54. data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +0 -1
  55. data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +0 -1
  56. data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +0 -1
  57. data/utils/enveomics/Pipelines/assembly.pbs/README.md +0 -189
  58. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +0 -112
  59. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +0 -23
  60. data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +0 -44
  61. data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +0 -50
  62. data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +0 -37
  63. data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +0 -68
  64. data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +0 -49
  65. data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +0 -80
  66. data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +0 -57
  67. data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +0 -63
  68. data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +0 -38
  69. data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +0 -73
  70. data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +0 -21
  71. data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +0 -72
  72. data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +0 -98
  73. data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +0 -1
  74. data/utils/enveomics/Pipelines/blast.pbs/README.md +0 -127
  75. data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +0 -109
  76. data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +0 -128
  77. data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +0 -16
  78. data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +0 -22
  79. data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +0 -26
  80. data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +0 -89
  81. data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +0 -29
  82. data/utils/enveomics/Pipelines/idba.pbs/README.md +0 -49
  83. data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +0 -95
  84. data/utils/enveomics/Pipelines/idba.pbs/run.pbs +0 -56
  85. data/utils/enveomics/Pipelines/trim.pbs/README.md +0 -54
  86. data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +0 -70
  87. data/utils/enveomics/Pipelines/trim.pbs/run.pbs +0 -130
  88. data/utils/enveomics/README.md +0 -42
  89. data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +0 -171
  90. data/utils/enveomics/Scripts/Aln.cat.rb +0 -163
  91. data/utils/enveomics/Scripts/Aln.convert.pl +0 -35
  92. data/utils/enveomics/Scripts/AlphaDiversity.pl +0 -152
  93. data/utils/enveomics/Scripts/BedGraph.tad.rb +0 -93
  94. data/utils/enveomics/Scripts/BedGraph.window.rb +0 -71
  95. data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +0 -102
  96. data/utils/enveomics/Scripts/BlastTab.addlen.rb +0 -63
  97. data/utils/enveomics/Scripts/BlastTab.advance.bash +0 -48
  98. data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +0 -55
  99. data/utils/enveomics/Scripts/BlastTab.catsbj.pl +0 -104
  100. data/utils/enveomics/Scripts/BlastTab.cogCat.rb +0 -76
  101. data/utils/enveomics/Scripts/BlastTab.filter.pl +0 -47
  102. data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +0 -194
  103. data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +0 -104
  104. data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +0 -157
  105. data/utils/enveomics/Scripts/BlastTab.recplot2.R +0 -48
  106. data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +0 -86
  107. data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +0 -119
  108. data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +0 -86
  109. data/utils/enveomics/Scripts/BlastTab.subsample.pl +0 -47
  110. data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +0 -114
  111. data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +0 -90
  112. data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +0 -101
  113. data/utils/enveomics/Scripts/Chao1.pl +0 -97
  114. data/utils/enveomics/Scripts/CharTable.classify.rb +0 -234
  115. data/utils/enveomics/Scripts/EBIseq2tax.rb +0 -83
  116. data/utils/enveomics/Scripts/FastA.N50.pl +0 -56
  117. data/utils/enveomics/Scripts/FastA.extract.rb +0 -152
  118. data/utils/enveomics/Scripts/FastA.filter.pl +0 -52
  119. data/utils/enveomics/Scripts/FastA.filterLen.pl +0 -28
  120. data/utils/enveomics/Scripts/FastA.filterN.pl +0 -60
  121. data/utils/enveomics/Scripts/FastA.fragment.rb +0 -92
  122. data/utils/enveomics/Scripts/FastA.gc.pl +0 -42
  123. data/utils/enveomics/Scripts/FastA.interpose.pl +0 -93
  124. data/utils/enveomics/Scripts/FastA.length.pl +0 -38
  125. data/utils/enveomics/Scripts/FastA.mask.rb +0 -89
  126. data/utils/enveomics/Scripts/FastA.per_file.pl +0 -36
  127. data/utils/enveomics/Scripts/FastA.qlen.pl +0 -57
  128. data/utils/enveomics/Scripts/FastA.rename.pl +0 -65
  129. data/utils/enveomics/Scripts/FastA.revcom.pl +0 -23
  130. data/utils/enveomics/Scripts/FastA.sample.rb +0 -83
  131. data/utils/enveomics/Scripts/FastA.slider.pl +0 -85
  132. data/utils/enveomics/Scripts/FastA.split.pl +0 -55
  133. data/utils/enveomics/Scripts/FastA.split.rb +0 -79
  134. data/utils/enveomics/Scripts/FastA.subsample.pl +0 -131
  135. data/utils/enveomics/Scripts/FastA.tag.rb +0 -65
  136. data/utils/enveomics/Scripts/FastA.wrap.rb +0 -48
  137. data/utils/enveomics/Scripts/FastQ.filter.pl +0 -54
  138. data/utils/enveomics/Scripts/FastQ.interpose.pl +0 -90
  139. data/utils/enveomics/Scripts/FastQ.offset.pl +0 -90
  140. data/utils/enveomics/Scripts/FastQ.split.pl +0 -53
  141. data/utils/enveomics/Scripts/FastQ.tag.rb +0 -63
  142. data/utils/enveomics/Scripts/FastQ.test-error.rb +0 -81
  143. data/utils/enveomics/Scripts/FastQ.toFastA.awk +0 -24
  144. data/utils/enveomics/Scripts/GFF.catsbj.pl +0 -127
  145. data/utils/enveomics/Scripts/GenBank.add_fields.rb +0 -84
  146. data/utils/enveomics/Scripts/HMM.essential.rb +0 -351
  147. data/utils/enveomics/Scripts/HMM.haai.rb +0 -168
  148. data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +0 -83
  149. data/utils/enveomics/Scripts/JPlace.distances.rb +0 -88
  150. data/utils/enveomics/Scripts/JPlace.to_iToL.rb +0 -320
  151. data/utils/enveomics/Scripts/M5nr.getSequences.rb +0 -81
  152. data/utils/enveomics/Scripts/MeTaxa.distribution.pl +0 -198
  153. data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +0 -35
  154. data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +0 -49
  155. data/utils/enveomics/Scripts/NCBIacc2tax.rb +0 -92
  156. data/utils/enveomics/Scripts/Newick.autoprune.R +0 -27
  157. data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +0 -228
  158. data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +0 -32
  159. data/utils/enveomics/Scripts/RefSeq.download.bash +0 -48
  160. data/utils/enveomics/Scripts/SRA.download.bash +0 -57
  161. data/utils/enveomics/Scripts/TRIBS.plot-test.R +0 -36
  162. data/utils/enveomics/Scripts/TRIBS.test.R +0 -39
  163. data/utils/enveomics/Scripts/Table.barplot.R +0 -31
  164. data/utils/enveomics/Scripts/Table.df2dist.R +0 -30
  165. data/utils/enveomics/Scripts/Table.filter.pl +0 -61
  166. data/utils/enveomics/Scripts/Table.merge.pl +0 -77
  167. data/utils/enveomics/Scripts/Table.replace.rb +0 -69
  168. data/utils/enveomics/Scripts/Table.round.rb +0 -63
  169. data/utils/enveomics/Scripts/Table.split.pl +0 -57
  170. data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +0 -227
  171. data/utils/enveomics/Scripts/VCF.KaKs.rb +0 -147
  172. data/utils/enveomics/Scripts/VCF.SNPs.rb +0 -88
  173. data/utils/enveomics/Scripts/aai.rb +0 -418
  174. data/utils/enveomics/Scripts/ani.rb +0 -362
  175. data/utils/enveomics/Scripts/clust.rand.rb +0 -102
  176. data/utils/enveomics/Scripts/gi2tax.rb +0 -103
  177. data/utils/enveomics/Scripts/in_silico_GA_GI.pl +0 -96
  178. data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
  179. data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
  180. data/utils/enveomics/Scripts/lib/enveomics.R +0 -1
  181. data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +0 -24
  182. data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +0 -253
  183. data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +0 -182
  184. data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +0 -74
  185. data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +0 -237
  186. data/utils/enveomics/Scripts/lib/enveomics_rb/stat.rb +0 -30
  187. data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +0 -135
  188. data/utils/enveomics/Scripts/ogs.annotate.rb +0 -88
  189. data/utils/enveomics/Scripts/ogs.core-pan.rb +0 -160
  190. data/utils/enveomics/Scripts/ogs.extract.rb +0 -125
  191. data/utils/enveomics/Scripts/ogs.mcl.rb +0 -186
  192. data/utils/enveomics/Scripts/ogs.rb +0 -104
  193. data/utils/enveomics/Scripts/ogs.stats.rb +0 -131
  194. data/utils/enveomics/Scripts/rbm.rb +0 -146
  195. data/utils/enveomics/Tests/Makefile +0 -10
  196. data/utils/enveomics/Tests/Mgen_M2288.faa +0 -3189
  197. data/utils/enveomics/Tests/Mgen_M2288.fna +0 -8282
  198. data/utils/enveomics/Tests/Mgen_M2321.fna +0 -8288
  199. data/utils/enveomics/Tests/Nequ_Kin4M.faa +0 -2970
  200. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
  201. data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +0 -7
  202. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +0 -17
  203. data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +0 -137
  204. data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +0 -123
  205. data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +0 -200
  206. data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +0 -55
  207. data/utils/enveomics/Tests/alkB.nwk +0 -1
  208. data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +0 -13
  209. data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +0 -17
  210. data/utils/enveomics/Tests/hiv1.faa +0 -59
  211. data/utils/enveomics/Tests/hiv1.fna +0 -134
  212. data/utils/enveomics/Tests/hiv2.faa +0 -70
  213. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +0 -233
  214. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +0 -1
  215. data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +0 -233
  216. data/utils/enveomics/Tests/phyla_counts.tsv +0 -10
  217. data/utils/enveomics/Tests/primate_lentivirus.ogs +0 -11
  218. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +0 -9
  219. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +0 -8
  220. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +0 -6
  221. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +0 -9
  222. data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +0 -6
  223. data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +0 -6
  224. data/utils/enveomics/build_enveomics_r.bash +0 -45
  225. data/utils/enveomics/enveomics.R/DESCRIPTION +0 -31
  226. data/utils/enveomics/enveomics.R/NAMESPACE +0 -39
  227. data/utils/enveomics/enveomics.R/R/autoprune.R +0 -155
  228. data/utils/enveomics/enveomics.R/R/barplot.R +0 -184
  229. data/utils/enveomics/enveomics.R/R/cliopts.R +0 -135
  230. data/utils/enveomics/enveomics.R/R/df2dist.R +0 -154
  231. data/utils/enveomics/enveomics.R/R/growthcurve.R +0 -331
  232. data/utils/enveomics/enveomics.R/R/recplot.R +0 -354
  233. data/utils/enveomics/enveomics.R/R/recplot2.R +0 -1631
  234. data/utils/enveomics/enveomics.R/R/tribs.R +0 -583
  235. data/utils/enveomics/enveomics.R/R/utils.R +0 -50
  236. data/utils/enveomics/enveomics.R/README.md +0 -80
  237. data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
  238. data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
  239. data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +0 -17
  240. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +0 -17
  241. data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +0 -17
  242. data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +0 -25
  243. data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +0 -46
  244. data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +0 -23
  245. data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +0 -47
  246. data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +0 -23
  247. data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +0 -23
  248. data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +0 -32
  249. data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +0 -91
  250. data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +0 -57
  251. data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +0 -24
  252. data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +0 -19
  253. data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +0 -39
  254. data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +0 -38
  255. data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +0 -40
  256. data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +0 -67
  257. data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +0 -37
  258. data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +0 -122
  259. data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +0 -45
  260. data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +0 -24
  261. data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +0 -68
  262. data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +0 -25
  263. data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +0 -21
  264. data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +0 -19
  265. data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +0 -19
  266. data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +0 -41
  267. data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +0 -29
  268. data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +0 -18
  269. data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +0 -40
  270. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +0 -36
  271. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +0 -19
  272. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +0 -19
  273. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +0 -27
  274. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +0 -41
  275. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +0 -17
  276. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +0 -43
  277. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +0 -37
  278. data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +0 -74
  279. data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +0 -59
  280. data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +0 -27
  281. data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +0 -32
  282. data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +0 -59
  283. data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +0 -28
  284. data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +0 -27
  285. data/utils/enveomics/enveomics.R/man/growth.curves.Rd +0 -14
  286. data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +0 -13
  287. data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +0 -63
  288. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +0 -38
  289. data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +0 -38
  290. data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +0 -111
  291. data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +0 -19
  292. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +0 -19
  293. data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +0 -19
  294. data/utils/enveomics/globals.mk +0 -8
  295. data/utils/enveomics/manifest.json +0 -9

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