miga-base 1.2.17.0 → 1.2.17.1
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- checksums.yaml +4 -4
- data/lib/miga/version.rb +1 -1
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm +41964 -0
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm +32439 -0
- data/utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm +62056 -0
- data/utils/FastAAI/FastAAI +3659 -0
- data/utils/FastAAI/FastAAI-legacy/FastAAI +1336 -0
- data/utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py +1296 -0
- data/utils/FastAAI/README.md +84 -0
- data/utils/enveomics/Docs/recplot2.md +244 -0
- data/utils/enveomics/Examples/aai-matrix.bash +66 -0
- data/utils/enveomics/Examples/ani-matrix.bash +66 -0
- data/utils/enveomics/Examples/essential-phylogeny.bash +105 -0
- data/utils/enveomics/Examples/unus-genome-phylogeny.bash +100 -0
- data/utils/enveomics/LICENSE.txt +73 -0
- data/utils/enveomics/Makefile +52 -0
- data/utils/enveomics/Manifest/Tasks/aasubs.json +103 -0
- data/utils/enveomics/Manifest/Tasks/blasttab.json +790 -0
- data/utils/enveomics/Manifest/Tasks/distances.json +161 -0
- data/utils/enveomics/Manifest/Tasks/fasta.json +802 -0
- data/utils/enveomics/Manifest/Tasks/fastq.json +291 -0
- data/utils/enveomics/Manifest/Tasks/graphics.json +126 -0
- data/utils/enveomics/Manifest/Tasks/mapping.json +137 -0
- data/utils/enveomics/Manifest/Tasks/ogs.json +382 -0
- data/utils/enveomics/Manifest/Tasks/other.json +906 -0
- data/utils/enveomics/Manifest/Tasks/remote.json +355 -0
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +650 -0
- data/utils/enveomics/Manifest/Tasks/tables.json +308 -0
- data/utils/enveomics/Manifest/Tasks/trees.json +68 -0
- data/utils/enveomics/Manifest/Tasks/variants.json +111 -0
- data/utils/enveomics/Manifest/categories.json +165 -0
- data/utils/enveomics/Manifest/examples.json +162 -0
- data/utils/enveomics/Manifest/tasks.json +4 -0
- data/utils/enveomics/Pipelines/assembly.pbs/CONFIG.mock.bash +69 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.N50.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.filterN.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/FastA.length.pl +1 -0
- data/utils/enveomics/Pipelines/assembly.pbs/README.md +189 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-2.bash +112 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-3.bash +23 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME-4.bash +44 -0
- data/utils/enveomics/Pipelines/assembly.pbs/RUNME.bash +50 -0
- data/utils/enveomics/Pipelines/assembly.pbs/kSelector.R +37 -0
- data/utils/enveomics/Pipelines/assembly.pbs/newbler.pbs +68 -0
- data/utils/enveomics/Pipelines/assembly.pbs/newbler_preparator.pl +49 -0
- data/utils/enveomics/Pipelines/assembly.pbs/soap.pbs +80 -0
- data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs +57 -0
- data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs +63 -0
- data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash +38 -0
- data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash +73 -0
- data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash +21 -0
- data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl +72 -0
- data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash +98 -0
- data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl +1 -0
- data/utils/enveomics/Pipelines/blast.pbs/README.md +127 -0
- data/utils/enveomics/Pipelines/blast.pbs/RUNME.bash +109 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.check.bash +128 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.dry.bash +16 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.eo.bash +22 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.pause.bash +26 -0
- data/utils/enveomics/Pipelines/blast.pbs/TASK.run.bash +89 -0
- data/utils/enveomics/Pipelines/blast.pbs/sentinel.pbs.bash +29 -0
- data/utils/enveomics/Pipelines/idba.pbs/README.md +49 -0
- data/utils/enveomics/Pipelines/idba.pbs/RUNME.bash +95 -0
- data/utils/enveomics/Pipelines/idba.pbs/run.pbs +56 -0
- data/utils/enveomics/Pipelines/trim.pbs/README.md +54 -0
- data/utils/enveomics/Pipelines/trim.pbs/RUNME.bash +70 -0
- data/utils/enveomics/Pipelines/trim.pbs/run.pbs +130 -0
- data/utils/enveomics/README.md +42 -0
- data/utils/enveomics/Scripts/AAsubs.log2ratio.rb +171 -0
- data/utils/enveomics/Scripts/Aln.cat.rb +221 -0
- data/utils/enveomics/Scripts/Aln.convert.pl +35 -0
- data/utils/enveomics/Scripts/AlphaDiversity.pl +152 -0
- data/utils/enveomics/Scripts/BedGraph.tad.rb +93 -0
- data/utils/enveomics/Scripts/BedGraph.window.rb +71 -0
- data/utils/enveomics/Scripts/BlastPairwise.AAsubs.pl +102 -0
- data/utils/enveomics/Scripts/BlastTab.addlen.rb +63 -0
- data/utils/enveomics/Scripts/BlastTab.advance.bash +48 -0
- data/utils/enveomics/Scripts/BlastTab.best_hit_sorted.pl +55 -0
- data/utils/enveomics/Scripts/BlastTab.catsbj.pl +104 -0
- data/utils/enveomics/Scripts/BlastTab.cogCat.rb +76 -0
- data/utils/enveomics/Scripts/BlastTab.filter.pl +47 -0
- data/utils/enveomics/Scripts/BlastTab.kegg_pep2path_rest.pl +194 -0
- data/utils/enveomics/Scripts/BlastTab.metaxaPrep.pl +104 -0
- data/utils/enveomics/Scripts/BlastTab.pairedHits.rb +157 -0
- data/utils/enveomics/Scripts/BlastTab.recplot2.R +48 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth.pl +86 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth_ZIP.pl +119 -0
- data/utils/enveomics/Scripts/BlastTab.seqdepth_nomedian.pl +86 -0
- data/utils/enveomics/Scripts/BlastTab.subsample.pl +47 -0
- data/utils/enveomics/Scripts/BlastTab.sumPerHit.pl +114 -0
- data/utils/enveomics/Scripts/BlastTab.taxid2taxrank.pl +90 -0
- data/utils/enveomics/Scripts/BlastTab.topHits_sorted.rb +123 -0
- data/utils/enveomics/Scripts/Chao1.pl +97 -0
- data/utils/enveomics/Scripts/CharTable.classify.rb +234 -0
- data/utils/enveomics/Scripts/EBIseq2tax.rb +83 -0
- data/utils/enveomics/Scripts/FastA.N50.pl +60 -0
- data/utils/enveomics/Scripts/FastA.extract.rb +152 -0
- data/utils/enveomics/Scripts/FastA.filter.pl +52 -0
- data/utils/enveomics/Scripts/FastA.filterLen.pl +28 -0
- data/utils/enveomics/Scripts/FastA.filterN.pl +60 -0
- data/utils/enveomics/Scripts/FastA.fragment.rb +100 -0
- data/utils/enveomics/Scripts/FastA.gc.pl +42 -0
- data/utils/enveomics/Scripts/FastA.interpose.pl +93 -0
- data/utils/enveomics/Scripts/FastA.length.pl +38 -0
- data/utils/enveomics/Scripts/FastA.mask.rb +89 -0
- data/utils/enveomics/Scripts/FastA.per_file.pl +36 -0
- data/utils/enveomics/Scripts/FastA.qlen.pl +57 -0
- data/utils/enveomics/Scripts/FastA.rename.pl +65 -0
- data/utils/enveomics/Scripts/FastA.revcom.pl +23 -0
- data/utils/enveomics/Scripts/FastA.sample.rb +98 -0
- data/utils/enveomics/Scripts/FastA.slider.pl +85 -0
- data/utils/enveomics/Scripts/FastA.split.pl +55 -0
- data/utils/enveomics/Scripts/FastA.split.rb +79 -0
- data/utils/enveomics/Scripts/FastA.subsample.pl +131 -0
- data/utils/enveomics/Scripts/FastA.tag.rb +65 -0
- data/utils/enveomics/Scripts/FastA.toFastQ.rb +69 -0
- data/utils/enveomics/Scripts/FastA.wrap.rb +48 -0
- data/utils/enveomics/Scripts/FastQ.filter.pl +54 -0
- data/utils/enveomics/Scripts/FastQ.interpose.pl +90 -0
- data/utils/enveomics/Scripts/FastQ.maskQual.rb +89 -0
- data/utils/enveomics/Scripts/FastQ.offset.pl +90 -0
- data/utils/enveomics/Scripts/FastQ.split.pl +53 -0
- data/utils/enveomics/Scripts/FastQ.tag.rb +70 -0
- data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
- data/utils/enveomics/Scripts/FastQ.toFastA.awk +24 -0
- data/utils/enveomics/Scripts/GFF.catsbj.pl +127 -0
- data/utils/enveomics/Scripts/GenBank.add_fields.rb +84 -0
- data/utils/enveomics/Scripts/HMM.essential.rb +351 -0
- data/utils/enveomics/Scripts/HMM.haai.rb +168 -0
- data/utils/enveomics/Scripts/HMMsearch.extractIds.rb +83 -0
- data/utils/enveomics/Scripts/JPlace.distances.rb +88 -0
- data/utils/enveomics/Scripts/JPlace.to_iToL.rb +320 -0
- data/utils/enveomics/Scripts/M5nr.getSequences.rb +81 -0
- data/utils/enveomics/Scripts/MeTaxa.distribution.pl +198 -0
- data/utils/enveomics/Scripts/MyTaxa.fragsByTax.pl +35 -0
- data/utils/enveomics/Scripts/MyTaxa.seq-taxrank.rb +49 -0
- data/utils/enveomics/Scripts/NCBIacc2tax.rb +92 -0
- data/utils/enveomics/Scripts/Newick.autoprune.R +27 -0
- data/utils/enveomics/Scripts/RAxML-EPA.to_iToL.pl +228 -0
- data/utils/enveomics/Scripts/RecPlot2.compareIdentities.R +32 -0
- data/utils/enveomics/Scripts/RefSeq.download.bash +48 -0
- data/utils/enveomics/Scripts/SRA.download.bash +55 -0
- data/utils/enveomics/Scripts/TRIBS.plot-test.R +36 -0
- data/utils/enveomics/Scripts/TRIBS.test.R +39 -0
- data/utils/enveomics/Scripts/Table.barplot.R +31 -0
- data/utils/enveomics/Scripts/Table.df2dist.R +30 -0
- data/utils/enveomics/Scripts/Table.filter.pl +61 -0
- data/utils/enveomics/Scripts/Table.merge.pl +77 -0
- data/utils/enveomics/Scripts/Table.prefScore.R +60 -0
- data/utils/enveomics/Scripts/Table.replace.rb +69 -0
- data/utils/enveomics/Scripts/Table.round.rb +63 -0
- data/utils/enveomics/Scripts/Table.split.pl +57 -0
- data/utils/enveomics/Scripts/Taxonomy.silva2ncbi.rb +227 -0
- data/utils/enveomics/Scripts/VCF.KaKs.rb +147 -0
- data/utils/enveomics/Scripts/VCF.SNPs.rb +88 -0
- data/utils/enveomics/Scripts/aai.rb +421 -0
- data/utils/enveomics/Scripts/ani.rb +362 -0
- data/utils/enveomics/Scripts/anir.rb +137 -0
- data/utils/enveomics/Scripts/clust.rand.rb +102 -0
- data/utils/enveomics/Scripts/gi2tax.rb +103 -0
- data/utils/enveomics/Scripts/in_silico_GA_GI.pl +96 -0
- data/utils/enveomics/Scripts/lib/data/dupont_2012_essential.hmm.gz +0 -0
- data/utils/enveomics/Scripts/lib/data/lee_2019_essential.hmm.gz +0 -0
- data/utils/enveomics/Scripts/lib/enveomics.R +1 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/anir.rb +293 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/bm_set.rb +175 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +24 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/errors.rb +17 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/gmm_em.rb +30 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +253 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/match.rb +88 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/og.rb +182 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/rbm.rb +49 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/remote_data.rb +74 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/seq_range.rb +237 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats/rand.rb +31 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats/sample.rb +152 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/stats.rb +3 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/utils.rb +74 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/vcf.rb +135 -0
- data/utils/enveomics/Scripts/ogs.annotate.rb +88 -0
- data/utils/enveomics/Scripts/ogs.core-pan.rb +160 -0
- data/utils/enveomics/Scripts/ogs.extract.rb +125 -0
- data/utils/enveomics/Scripts/ogs.mcl.rb +186 -0
- data/utils/enveomics/Scripts/ogs.rb +104 -0
- data/utils/enveomics/Scripts/ogs.stats.rb +131 -0
- data/utils/enveomics/Scripts/rbm-legacy.rb +172 -0
- data/utils/enveomics/Scripts/rbm.rb +108 -0
- data/utils/enveomics/Scripts/sam.filter.rb +148 -0
- data/utils/enveomics/Tests/Makefile +10 -0
- data/utils/enveomics/Tests/Mgen_M2288.faa +3189 -0
- data/utils/enveomics/Tests/Mgen_M2288.fna +8282 -0
- data/utils/enveomics/Tests/Mgen_M2321.fna +8288 -0
- data/utils/enveomics/Tests/Nequ_Kin4M.faa +2970 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.tribs.Rdata +0 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae-PilA.txt +7 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae.aai-mat.tsv +17 -0
- data/utils/enveomics/Tests/Xanthomonas_oryzae.aai.tsv +137 -0
- data/utils/enveomics/Tests/a_mg.cds-go.blast.tsv +123 -0
- data/utils/enveomics/Tests/a_mg.reads-cds.blast.tsv +200 -0
- data/utils/enveomics/Tests/a_mg.reads-cds.counts.tsv +55 -0
- data/utils/enveomics/Tests/alkB.nwk +1 -0
- data/utils/enveomics/Tests/anthrax-cansnp-data.tsv +13 -0
- data/utils/enveomics/Tests/anthrax-cansnp-key.tsv +17 -0
- data/utils/enveomics/Tests/hiv1.faa +59 -0
- data/utils/enveomics/Tests/hiv1.fna +134 -0
- data/utils/enveomics/Tests/hiv2.faa +70 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv +233 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.lim +1 -0
- data/utils/enveomics/Tests/hiv_mix-hiv1.blast.tsv.rec +233 -0
- data/utils/enveomics/Tests/phyla_counts.tsv +10 -0
- data/utils/enveomics/Tests/primate_lentivirus.ogs +11 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv1.rbm +9 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-hiv2.rbm +8 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv1-siv.rbm +6 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-hiv2.rbm +9 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/hiv2-siv.rbm +6 -0
- data/utils/enveomics/Tests/primate_lentivirus.rbm/siv-siv.rbm +6 -0
- data/utils/enveomics/build_enveomics_r.bash +45 -0
- data/utils/enveomics/enveomics.R/DESCRIPTION +31 -0
- data/utils/enveomics/enveomics.R/NAMESPACE +39 -0
- data/utils/enveomics/enveomics.R/R/autoprune.R +155 -0
- data/utils/enveomics/enveomics.R/R/barplot.R +184 -0
- data/utils/enveomics/enveomics.R/R/cliopts.R +135 -0
- data/utils/enveomics/enveomics.R/R/df2dist.R +154 -0
- data/utils/enveomics/enveomics.R/R/growthcurve.R +331 -0
- data/utils/enveomics/enveomics.R/R/prefscore.R +79 -0
- data/utils/enveomics/enveomics.R/R/recplot.R +354 -0
- data/utils/enveomics/enveomics.R/R/recplot2.R +1631 -0
- data/utils/enveomics/enveomics.R/R/tribs.R +583 -0
- data/utils/enveomics/enveomics.R/R/utils.R +80 -0
- data/utils/enveomics/enveomics.R/README.md +81 -0
- data/utils/enveomics/enveomics.R/data/growth.curves.rda +0 -0
- data/utils/enveomics/enveomics.R/data/phyla.counts.rda +0 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.GrowthCurve-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/cash-enve.RecPlot2.Peak-method.Rd +16 -0
- data/utils/enveomics/enveomics.R/man/enve.GrowthCurve-class.Rd +25 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBS-class.Rd +46 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBS.merge.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.TRIBStest-class.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.__prune.iter.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.__prune.reduce.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.__tribs.Rd +40 -0
- data/utils/enveomics/enveomics.R/man/enve.barplot.Rd +103 -0
- data/utils/enveomics/enveomics.R/man/enve.cliopts.Rd +67 -0
- data/utils/enveomics/enveomics.R/man/enve.col.alpha.Rd +24 -0
- data/utils/enveomics/enveomics.R/man/enve.col2alpha.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.group.Rd +44 -0
- data/utils/enveomics/enveomics.R/man/enve.df2dist.list.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.growthcurve.Rd +75 -0
- data/utils/enveomics/enveomics.R/man/enve.prefscore.Rd +50 -0
- data/utils/enveomics/enveomics.R/man/enve.prune.dist.Rd +44 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot.Rd +139 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2-class.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.ANIr.Rd +24 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.Rd +77 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__counts.Rd +25 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__peakHist.Rd +21 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.__whichClosestPeak.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.changeCutoff.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.compareIdentities.Rd +47 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.coordinates.Rd +29 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.corePeak.Rd +18 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.extractWindows.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.Rd +36 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_e.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__em_m.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__emauto_one.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mow_one.Rd +52 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd +17 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd +51 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd +43 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd +82 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd +59 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/enve.recplot2.windowDepthThreshold.Rd +36 -0
- data/utils/enveomics/enveomics.R/man/enve.selvector.Rd +23 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.Rd +68 -0
- data/utils/enveomics/enveomics.R/man/enve.tribs.test.Rd +28 -0
- data/utils/enveomics/enveomics.R/man/enve.truncate.Rd +27 -0
- data/utils/enveomics/enveomics.R/man/growth.curves.Rd +14 -0
- data/utils/enveomics/enveomics.R/man/phyla.counts.Rd +13 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.GrowthCurve.Rd +78 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBS.Rd +46 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.TRIBStest.Rd +45 -0
- data/utils/enveomics/enveomics.R/man/plot.enve.recplot2.Rd +125 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.GrowthCurve.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBS.Rd +19 -0
- data/utils/enveomics/enveomics.R/man/summary.enve.TRIBStest.Rd +19 -0
- data/utils/enveomics/globals.mk +8 -0
- data/utils/enveomics/manifest.json +9 -0
- data/utils/multitrim/Multitrim How-To.pdf +0 -0
- data/utils/multitrim/README.md +67 -0
- data/utils/multitrim/multitrim.py +1555 -0
- data/utils/multitrim/multitrim.yml +13 -0
- metadata +301 -5
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{
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"tasks": [
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{
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"task": "Aln.cat.rb",
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"description": ["Concatenates several multiple alignments in FastA",
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"format into a single multiple alignment. The IDs of the sequences",
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"(or the ID prefixes, if using --ignore-after) must coincide across",
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"files."],
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"help_arg": "--help",
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"options": [
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{
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"opt": "--coords",
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"arg": "out_file",
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"description": "Output file of coordinates in RAxML-compliant format."
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},
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{
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"opt": "--ignore-after",
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"arg": "string",
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"description": ["Remove everything in the IDs after the specified",
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"string."]
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},
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{
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"opt": "--remove-invariable",
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"description": "Remove invariable sites.",
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"note": ["Invariable sites are defined as columns with only one",
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"state and undefined characters. Additional ambiguous characters",
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"may exist and should be declared using --undefined."]
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"opt": "--missing-char",
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"description": "Character denoting missing data.",
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"arg": "character",
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"default": "-"
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},
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{
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"opt": "--model",
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"description": "Name of the model to use if --coords is used.",
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"note": "See RAxML's documentation for additional information.",
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"arg": "string",
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"default": "AUTO"
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},
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{
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"opt": "--undefined",
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"arg": "string",
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"description": ["All characters to be regarded as 'undefined'. It",
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"should include all ambiguous and missing data chars. Ignored",
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"unless --remove-invariable."],
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"default": "-.Xx?"
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},
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{
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"opt": "--quiet",
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"description": "Run quietly (no STDERR output)."
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},
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{
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"name": "Input alignments",
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"arg": "in_file",
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"multiple_sep": " ",
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"mandatory": true,
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"description": "Input alignments in FastA format."
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},
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">",
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{
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"name": "Output alignment",
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"arg": "out_file",
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"mandatory": true,
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"description": "Output concatenated alignment."
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}
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]
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},
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{
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"task": "Aln.convert.pl",
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"description": "Translates between different alignment formats.",
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"help_arg": "",
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"requires": [
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{
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"perl_lib": "Bio::AlignIO"
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}
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],
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"cite": [["Stajich et al, 2002, GRes",
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"http://dx.doi.org/10.1101/gr.361602"]],
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"options": [
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{
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"name": "In-format",
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"description": "Input file's format.",
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"mandatory": true,
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"arg": "select",
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"values": ["bl2seq", "clustalw", "emboss", "fasta", "maf", "mase",
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"mega", "meme", "metafasta", "msf", "nexus", "pfam", "phylip", "po",
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"prodom", "psi", "selex", "stockholm", "XMFA", "arp"]
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},
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{
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"name": "Out-format",
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"description": "Output file's format.",
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"mandatory": true,
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"arg": "select",
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"values": ["bl2seq", "clustalw", "emboss", "fasta", "maf", "mase",
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"mega", "meme", "metafasta", "msf", "nexus", "pfam", "phylip", "po",
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"prodom", "psi", "selex", "stockholm", "XMFA", "arp"]
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},
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"<",
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"arg": "in_file",
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"mandatory": true
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},
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">",
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{
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"arg": "out_file",
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"mandatory": true
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]
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},
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{
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"task": "AlphaDiversity.pl",
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"description": ["Takes a table of OTU abundance in one or more samples",
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"and calculates the Rao (Q_alpha), Rao-Jost (Q_alpha_eqv), Shannon",
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"(Hprime), and inverse Simpson (1_lambda) indices of alpha diversity",
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"for each sample."],
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"help_arg": "--help",
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"see_also": ["Chao1.pl"],
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"options": [
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{
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"name": "Input table",
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"opt": "-i",
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"arg": "in_file",
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"description": ["Columns: samples, rows: OTUs, first column: OTU",
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"names)."],
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"mandatory": true
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{
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"name": "Discard rows",
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"opt": "-r",
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"arg": "integer",
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"description": "Number of rows to ignore.",
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"default": 0
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},
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{
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"name": "Discard left columns",
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"opt": "-c",
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"arg": "integer",
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"description": ["Number of columns to ignore after the first column",
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"(i.e., between the first column, containing the name of the",
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"categories, and the first column of abundance values)."],
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"default": 0
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},
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{
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"name": "Discard right columns",
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"opt": "-C",
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"arg": "integer",
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"description": "Number of columns to ignore at the end of each line.",
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"default": 0
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},
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{
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"name": "Delimiter",
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"opt": "-d",
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"arg": "string",
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"description": "Character (or string) separating columns.",
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"note": ["Supported escaped characters are: '\\t' (tabulation), and",
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"'\\0' (null bit)."],
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"default": "\\t"
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},
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{
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"name": "Headers",
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"opt": "-h",
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"description": ["The first row is assumed to have the names of the",
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"samples."]
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},
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{
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"name": "Distances file",
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"opt": "-D",
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"arg": "in_file",
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"description": ["A squared matrix (or bottom-left half matrix) with",
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"the distances between categories (OTUs or functions). The first",
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"column must contain the names of the categories, and it shouldn't",
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"have headers. If not set, all distances are assumed to be one."],
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"note": "Only used for Rao."
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{
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"name": "Skip Rao",
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"opt": "-R",
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"description": "Do not calculate Rao indices.",
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"note": ["This significantly decreases the total running time. Note",
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"that Rao indices are highly susceptible to precision errors, and",
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"shouldn't be trusted for very big numbers."]
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},
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{
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"name": "q for qD",
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"opt": "-q",
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"arg": "integer",
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"description": "Estimate the qD index (true diversity order q).",
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"default": 0
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},
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">",
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{
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"arg": "out_file",
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"mandatory": true
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}
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]
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},
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{
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"task": "Chao1.pl",
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"description": ["Takes a table of OTU abundance in one or more samples",
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"and calculates the chao1 index (with 95% Confidence Interval) for",
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"each sample. To use it with Qiime OTU Tables, run it ignoring 1",
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"left column and with header."],
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"cite": [["Chao, 1984, Scandinavian J Stat",
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"http://www.jstor.org/stable/4615964"]],
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"see_also": ["AlphaDiversity.pl"],
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"help_arg": "--help",
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"options": [
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{
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"name": "Input file",
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"opt": "-i",
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"arg": "in_file",
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"mandatory": true,
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"description": "Input table (columns:samples, rows:OTUs)."
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},
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{
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"name": "Rows",
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"opt": "-r",
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"arg": "integer",
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"default": 0,
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"description": "Number of rows to ignore."
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},
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{
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"name": "Left columns to ignore",
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"opt": "-c",
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"arg": "integer",
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"default": 0,
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"description": "Number of columns to ignore."
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},
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{
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"name": "Right columns to ignore",
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"opt": "-C",
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"arg": "integer",
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"default": 0,
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"description": "Number of columns to ignore at the end."
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},
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{
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"name": "Delimiter",
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"opt": "-d",
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"arg": "string",
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"default": "\\t",
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"description": "Delimiter between columns.",
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"note": ["Supported escaped characters are: \\t (tabulation),",
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"and \\0 (null bit)."]
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},
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{
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"name": "Header",
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"opt": "-h",
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"description": ["If set, the first row is assumed to have the names",
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"of the samples."]
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},
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">",
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{
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"arg": "out_file",
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"mandatory": true,
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"description": ["Chao1 index and 95% CI bounds for each sample, in",
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"tab-delimited format."]
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}
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]
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},
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{
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"task": "CharTable.classify.rb",
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"description": ["Uses a dichotomous key to classify objects parsing a",
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"character table."],
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"help_arg": "--help",
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"options": [
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{
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"opt": "--table",
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"arg": "in_file",
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"mandatory": true,
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"description": ["Input table containing the states (columns) per",
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"object (row). It must be tab-delimited and with row and column",
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"names."]
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},
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{
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"opt": "--key",
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"arg": "in_file",
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"mandatory": true,
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"description": ["Input table containing the dychotomous key in",
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"linked style, defined in four columns (can contain #-lead comment",
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"lines): (1) ID of the step, typically a sequential integer. (2)",
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"Name of character to evaluate. Must coincide with the -t headers.",
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"(3) First character decision (see below). (4) Second character",
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"decision (see below).\nA character decision must be formated as:",
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"state (must coincide with the values in -t), colon (:), step to",
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"follow. If the state is * (star) any state triggers the decision",
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"(this should be the norm in column 4). The step to follow should",
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"be a step ID in square brackets, or the name of the",
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"classification."]
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},
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{
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"opt": "--classification",
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"arg": "out_file",
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"description": ["Two-column table with the classification of the",
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"input objects."]
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},
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{
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"opt": "--newick",
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"arg": "out_file",
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"description": ["Tree containing all the classified objects. This",
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"only makes sense for synoptic keys."]
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},
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{
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"opt": "--quiet",
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"description": "Run quietly (no STDERR output)."
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}
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]
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},
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{
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"task": "GenBank.add_fields.rb",
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"description": "Adds annotations to GenBank files.",
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"help_arg": "--help",
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"options": [
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{
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"opt": "--genbank",
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"arg": "in_file",
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"mandatory": true,
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"description": "Input GenBank file."
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},
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{
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"opt": "--table",
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"arg": "in_file",
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"mandatory": true,
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"description": ["Input file containing the annotations. It must be a",
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"tab-delimited raw table including a header row with the names of",
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"the fields."]
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},
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{
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"opt": "--out",
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"arg": "out_file",
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"mandatory": true,
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"description": "Output file containing the annotated GenBank."
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},
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{
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"opt": "--key",
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"arg": "integer",
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"default": 1,
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"description": "Key of the column to use as identifier."
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},
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{
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"opt": "--split",
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"arg": "string",
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"default": "#",
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"description": ["String that separates multiple entries in the",
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"annotation features."]
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},
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{
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"opt": "--quiet",
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"description": "Run quietly (no STDERR output)."
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}
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]
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},
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{
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"task": "HMM.essential.rb",
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"description": ["Finds and extracts a collection of essential proteins",
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"suitable for genome completeness evaluation and phylogenetic",
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"analyses in Archaea and Bacteria."],
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"warn": ["Most complete bacterial genomes contain only 106/111 genes in",
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"this collection, therefore producing a completeness of 95.5%, and",
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"most archaeal genomes only contain 26/111 genes, producing a",
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"completeness of 23.4%. Use the options --bacteria and/or --archaea to",
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"ignore models often missing in one or both domains. Note that even",
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"with these options, some complete archaeal genomes result in very low",
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"values of completeness (e.g., Nanoarchaeum equitans returns 88.5%)."],
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"help_arg": "--help",
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"requires": [
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{
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"description": "HMMer 3.0+",
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370
|
+
"test": "hmmsearch -h",
|
371
|
+
"source_url": "http://hmmer.janelia.org/software"
|
372
|
+
}
|
373
|
+
],
|
374
|
+
"cite": [
|
375
|
+
["Eddy, 2011, PLoS CB",
|
376
|
+
"http://dx.doi.org/10.1371/journal.pcbi.1002195"],
|
377
|
+
["Dupont et al, 2012, ISME J",
|
378
|
+
"https://doi.org/10.1038/ismej.2011.189"],
|
379
|
+
["Rodriguez-R et al, 2014, ISME J",
|
380
|
+
"https://doi.org/10.1038/ismej.2015.5"],
|
381
|
+
["Lee, 2019, Bioinf",
|
382
|
+
"https://doi.org/10.1093/bioinformatics/btz188"],
|
383
|
+
["Eren et al, 2015, PeerJ",
|
384
|
+
"https://doi.org/10.7717/peerj.1319"]
|
385
|
+
],
|
386
|
+
"options": [
|
387
|
+
{
|
388
|
+
"name": "Input file",
|
389
|
+
"opt": "--in",
|
390
|
+
"arg": "in_file",
|
391
|
+
"mandatory": true,
|
392
|
+
"description": "FastA file containing all the proteins in the genome."
|
393
|
+
},
|
394
|
+
{
|
395
|
+
"opt": "--collection",
|
396
|
+
"arg": "string",
|
397
|
+
"default": "dupont_2012",
|
398
|
+
"description": ["Reference collection of essential proteins to use.",
|
399
|
+
"One of: dupont_2012 (default, Dupont et al 2012 modified by",
|
400
|
+
"Rodriguez-R et al 2015), or lee_2019 (Lee 2019 modified by Eren",
|
401
|
+
"et al 2015)."]
|
402
|
+
},
|
403
|
+
{
|
404
|
+
"name": "Output file",
|
405
|
+
"opt": "--out",
|
406
|
+
"arg": "out_file",
|
407
|
+
"description": ["FastA file with the translated essential genes. By",
|
408
|
+
"default the file is not produced."]
|
409
|
+
},
|
410
|
+
{
|
411
|
+
"opt": "--per-model",
|
412
|
+
"arg": "out_file",
|
413
|
+
"description": ["Prefix of translated genes in independent files",
|
414
|
+
"with the name of the model appended. By default files are not",
|
415
|
+
"produced."]
|
416
|
+
},
|
417
|
+
{
|
418
|
+
"opt": "--report",
|
419
|
+
"arg": "out_file",
|
420
|
+
"description": ["Path to the report file. By default, the report is",
|
421
|
+
"sent to the STDOUT."]
|
422
|
+
},
|
423
|
+
{
|
424
|
+
"name": "HMMsearch output",
|
425
|
+
"opt": "--hmm-out",
|
426
|
+
"arg": "out_file",
|
427
|
+
"description": ["Save HMMsearch output in this file. By default,",
|
428
|
+
"not saved."]
|
429
|
+
},
|
430
|
+
{
|
431
|
+
"opt": "--alignments",
|
432
|
+
"opt": "out_file",
|
433
|
+
"description": ["Save the aligned proteins in this file. By default,",
|
434
|
+
"not saved."]
|
435
|
+
},
|
436
|
+
{
|
437
|
+
"opt": "--bacteria",
|
438
|
+
"description": "If set, ignores models typically missing in Bacteria."
|
439
|
+
},
|
440
|
+
{
|
441
|
+
"opt": "--archaea",
|
442
|
+
"description": "If set, ignores models typically missing in Archaea."
|
443
|
+
},
|
444
|
+
{
|
445
|
+
"opt": "--genome-eq",
|
446
|
+
"description": ["If set, ignores models not suitable for",
|
447
|
+
"genome-equivalents estimations. See Rodriguez-R et al, 2015, ISME",
|
448
|
+
"J 9(9):1928-1940."],
|
449
|
+
"source_url": "http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej20155a.html"
|
450
|
+
},
|
451
|
+
{
|
452
|
+
"opt": "--rename",
|
453
|
+
"arg": "string",
|
454
|
+
"description": ["If set, renames the sequences with the string",
|
455
|
+
"provided and appends it with pipe (|) and the gene name (except",
|
456
|
+
"in --per-model files)."]
|
457
|
+
},
|
458
|
+
{
|
459
|
+
"opt": "--no-stats",
|
460
|
+
"description": ["If set, no statistics are reported on genome",
|
461
|
+
"evaluation."]
|
462
|
+
},
|
463
|
+
{
|
464
|
+
"opt": "--no-genes",
|
465
|
+
"description": ["If set, statistics won't include the lists of",
|
466
|
+
"missing/multi-copy genes."]
|
467
|
+
},
|
468
|
+
{
|
469
|
+
"opt": "--metagenome",
|
470
|
+
"description": ["If set, it allows for multiple copies of each gene",
|
471
|
+
"and turns on metagenomic report mode."]
|
472
|
+
},
|
473
|
+
{
|
474
|
+
"opt": "--list-models",
|
475
|
+
"description": ["If set, it only lists the models and exits.",
|
476
|
+
"Compatible with 'Archaea', 'Bacteria', 'Genome eq', and 'Quiet';",
|
477
|
+
"ignores all other parameters."]
|
478
|
+
},
|
479
|
+
{
|
480
|
+
"opt": "--bin",
|
481
|
+
"arg": "in_dir",
|
482
|
+
"description": "Directory containing the binaries of HMMer 3.0+."
|
483
|
+
},
|
484
|
+
{
|
485
|
+
"opt": "--model-file",
|
486
|
+
"arg": "in_file",
|
487
|
+
"description": "External file containing models to search."
|
488
|
+
},
|
489
|
+
{
|
490
|
+
"opt": "--threads",
|
491
|
+
"arg": "integer",
|
492
|
+
"default": 2,
|
493
|
+
"description": "Number of parallel threads to be used."
|
494
|
+
},
|
495
|
+
{
|
496
|
+
"opt": "--quiet",
|
497
|
+
"description": "Run quietly (no STDERR output)."
|
498
|
+
}
|
499
|
+
]
|
500
|
+
},
|
501
|
+
{
|
502
|
+
"task": "HMMsearch.extractIds.rb",
|
503
|
+
"description": ["Extracts the sequence IDs and query model form a",
|
504
|
+
"(multiple) HMMsearch report (for HMMer 3.0)."],
|
505
|
+
"help_arg": "--help",
|
506
|
+
"options": [
|
507
|
+
{
|
508
|
+
"opt": "--all-evalue",
|
509
|
+
"arg": "float",
|
510
|
+
"description": "Maximum e-value of sequence to report result."
|
511
|
+
},
|
512
|
+
{
|
513
|
+
"opt": "--all-score",
|
514
|
+
"arg": "float",
|
515
|
+
"description": "Minimum score of sequence to report result."
|
516
|
+
},
|
517
|
+
{
|
518
|
+
"opt": "--best-evalue",
|
519
|
+
"arg": "float",
|
520
|
+
"description": "Maximum e-value of best domain to report result."
|
521
|
+
},
|
522
|
+
{
|
523
|
+
"opt": "--best-score",
|
524
|
+
"arg": "float",
|
525
|
+
"description": "Minimum score of best domain to report result."
|
526
|
+
},
|
527
|
+
{
|
528
|
+
"opt": "--no-model",
|
529
|
+
"description": "Do not include the query model in the output list."
|
530
|
+
},
|
531
|
+
{
|
532
|
+
"opt": "--quiet",
|
533
|
+
"description": "Run quietly."
|
534
|
+
},
|
535
|
+
"<",
|
536
|
+
{
|
537
|
+
"arg": "in_file",
|
538
|
+
"mandatory": true,
|
539
|
+
"description": "Input HMMsearch text file."
|
540
|
+
},
|
541
|
+
">",
|
542
|
+
{
|
543
|
+
"arg": "out_file",
|
544
|
+
"mandatory": true,
|
545
|
+
"description": "Output list of IDs."
|
546
|
+
}
|
547
|
+
]
|
548
|
+
},
|
549
|
+
{
|
550
|
+
"task": "JPlace.distances.rb",
|
551
|
+
"description": ["Extracts the distance (estimated branch length) of each",
|
552
|
+
"placed read to a given node in a JPlace file."],
|
553
|
+
"requires": [ { "ruby_gem": "json" } ],
|
554
|
+
"help_arg": "--help",
|
555
|
+
"options": [
|
556
|
+
{
|
557
|
+
"name": "Input file",
|
558
|
+
"opt": "--in",
|
559
|
+
"arg": "in_file",
|
560
|
+
"mandatory": true,
|
561
|
+
"description": ".jplace input file containing the read placement."
|
562
|
+
},
|
563
|
+
{
|
564
|
+
"name": "Node",
|
565
|
+
"opt": "--node",
|
566
|
+
"arg": "string",
|
567
|
+
"mandatory": true,
|
568
|
+
"description": ["Index (number in curly brackets) of the node to",
|
569
|
+
"which distances should be measured."]
|
570
|
+
},
|
571
|
+
{
|
572
|
+
"name": "Output file",
|
573
|
+
"opt": "--out",
|
574
|
+
"arg": "out_file",
|
575
|
+
"mandatory": true,
|
576
|
+
"description": "Output file in tabular format."
|
577
|
+
},
|
578
|
+
{
|
579
|
+
"opt": "--in-node",
|
580
|
+
"arg": "string",
|
581
|
+
"description": ["Report only reads placed at this node or it's",
|
582
|
+
"children."]
|
583
|
+
},
|
584
|
+
{
|
585
|
+
"opt": "--quiet",
|
586
|
+
"description": "Run quietly (no STDERR output)."
|
587
|
+
}
|
588
|
+
]
|
589
|
+
},
|
590
|
+
{
|
591
|
+
"task": "JPlace.to_iToL.rb",
|
592
|
+
"description": ["Generates iToL-compatible files from a .jplace file",
|
593
|
+
"(produced by RAxML's EPA or pplacer), that can be used to draw",
|
594
|
+
"pie-charts in the nodes of the reference tree."],
|
595
|
+
"requires": [ { "ruby_gem": "json" } ],
|
596
|
+
"help_arg": "--help",
|
597
|
+
"options": [
|
598
|
+
{
|
599
|
+
"name": "Input file",
|
600
|
+
"opt": "--in",
|
601
|
+
"arg": "in_file",
|
602
|
+
"mandatory": true,
|
603
|
+
"description": ".jplace input file containing the read placement."
|
604
|
+
},
|
605
|
+
{
|
606
|
+
"name": "Out base",
|
607
|
+
"opt": "--out",
|
608
|
+
"arg": "out_file",
|
609
|
+
"mandatory": true,
|
610
|
+
"description": "Base of the output files."
|
611
|
+
},
|
612
|
+
{
|
613
|
+
"opt": "--unique",
|
614
|
+
"arg": "string",
|
615
|
+
"description": ["Name of the dataset (if only one is used).",
|
616
|
+
"Conflicts with 'Regex' and 'Separator'."]
|
617
|
+
},
|
618
|
+
{
|
619
|
+
"opt": "--regex",
|
620
|
+
"arg": "string",
|
621
|
+
"description": ["Regular expression capturing the sample ID (named",
|
622
|
+
"dataset) in read names. By default: '^(?<dataset>.+?):.*'.",
|
623
|
+
"Conflicts with 'Separator'."]
|
624
|
+
},
|
625
|
+
{
|
626
|
+
"opt": "--separator",
|
627
|
+
"arg": "string",
|
628
|
+
"description": ["String separating the dataset name and the rest of",
|
629
|
+
"the read name. It assumes that the read name starts by the",
|
630
|
+
"dataset name. Conflicts with 'Regex'."]
|
631
|
+
},
|
632
|
+
{
|
633
|
+
"opt": "--metadata",
|
634
|
+
"arg": "in_file",
|
635
|
+
"description": ["Datasets metadata in tab-delimited format with a",
|
636
|
+
"header row. Valid headers: name (required), color (in Hex),",
|
637
|
+
"size (# reads), norm (any float)."]
|
638
|
+
},
|
639
|
+
{
|
640
|
+
"opt": "--norm",
|
641
|
+
"arg": "string",
|
642
|
+
"description": ["Normalization strategy. Must be one of:\n",
|
643
|
+
"none: Direct read counts are reported without normalization.\n",
|
644
|
+
"count (default): The counts are normalized (divided) by the total",
|
645
|
+
"counts per dataset.\n",
|
646
|
+
"size: The counts are normalized (divided) by the size column in",
|
647
|
+
"metadata (must be integer).\n",
|
648
|
+
"norm: The counts are normalized (divided) by the norm column in",
|
649
|
+
"metadata (can be any float)."]
|
650
|
+
},
|
651
|
+
{
|
652
|
+
"opt": "--old-itol",
|
653
|
+
"description": ["Generate output file using the old iToL format",
|
654
|
+
" (pre v3.0)."]
|
655
|
+
},
|
656
|
+
{
|
657
|
+
"opt": "--collapse",
|
658
|
+
"arg": "in_file",
|
659
|
+
"description": "Internal nodes to collapse (requires rootted tree)."
|
660
|
+
},
|
661
|
+
{
|
662
|
+
"opt": "--area",
|
663
|
+
"description": ["If set, the area of the pies is proportional to the",
|
664
|
+
"placements. Otherwise, the radius is."]
|
665
|
+
},
|
666
|
+
{
|
667
|
+
"opt": "--quiet",
|
668
|
+
"description": "Run quietly (no STDERR output)."
|
669
|
+
}
|
670
|
+
]
|
671
|
+
},
|
672
|
+
{
|
673
|
+
"task": "MyTaxa.fragsByTax.pl",
|
674
|
+
"description": "Identifies fragments annotated as a taxon in MyTaxa.",
|
675
|
+
"help_arg": "",
|
676
|
+
"options": [
|
677
|
+
{
|
678
|
+
"name": "MyTaxa output",
|
679
|
+
"arg": "in_file",
|
680
|
+
"mandatory": true,
|
681
|
+
"description": "Classification file generated by MyTaxa."
|
682
|
+
},
|
683
|
+
{
|
684
|
+
"name": "Taxon",
|
685
|
+
"arg": "string",
|
686
|
+
"mandatory": true,
|
687
|
+
"description": "Taxon to look for."
|
688
|
+
},
|
689
|
+
{
|
690
|
+
"name": "Rank",
|
691
|
+
"arg": "string",
|
692
|
+
"description": "Rank of taxon (optional). By default: any rank."
|
693
|
+
},
|
694
|
+
">",
|
695
|
+
{
|
696
|
+
"arg": "out_file",
|
697
|
+
"mandatory": true,
|
698
|
+
"description": "List of fragment IDs."
|
699
|
+
}
|
700
|
+
]
|
701
|
+
},
|
702
|
+
{
|
703
|
+
"task": "MyTaxa.seq-taxrank.rb",
|
704
|
+
"description": ["Generates a simple tabular file with the classification",
|
705
|
+
"of each sequence at a given taxonomic rank from a MyTaxa output."],
|
706
|
+
"help_arg": "--help",
|
707
|
+
"options": [
|
708
|
+
{
|
709
|
+
"name": "MyTaxa",
|
710
|
+
"opt": "--mytaxa",
|
711
|
+
"arg": "in_file",
|
712
|
+
"mandatory": true,
|
713
|
+
"description": "Input MyTaxa file."
|
714
|
+
},
|
715
|
+
{
|
716
|
+
"opt": "--rank",
|
717
|
+
"arg": "string",
|
718
|
+
"default": "genus",
|
719
|
+
"description": "Taxonomic rank."
|
720
|
+
},
|
721
|
+
{
|
722
|
+
"opt": "--quiet",
|
723
|
+
"description": "Run quietly."
|
724
|
+
}
|
725
|
+
]
|
726
|
+
},
|
727
|
+
{
|
728
|
+
"task": "Taxonomy.silva2ncbi.rb",
|
729
|
+
"description": ["Re-formats Silva taxonomy into NCBI-like taxonomy dump",
|
730
|
+
"files."],
|
731
|
+
"help_arg": "--help",
|
732
|
+
"options": [
|
733
|
+
{
|
734
|
+
"opt": "--silvaranks",
|
735
|
+
"arg": "in_file",
|
736
|
+
"mandatory": true,
|
737
|
+
"description": ["Input Silva ranks file (e.g.,",
|
738
|
+
"tax_ranks_ssu_115.txt)."],
|
739
|
+
"source_url": "https://www.arb-silva.de/no_cache/download/archive/release_115/Exports/"
|
740
|
+
},
|
741
|
+
{
|
742
|
+
"opt": "--silvaref",
|
743
|
+
"arg": "in_file",
|
744
|
+
"mandatory": true,
|
745
|
+
"description": ["Input Silva ref alignment file (e.g.,",
|
746
|
+
"SSURef_NR99_115_tax_silva_full_align_trunc.fasta)."],
|
747
|
+
"source_url": "https://www.arb-silva.de/no_cache/download/archive/release_115/Exports/"
|
748
|
+
},
|
749
|
+
{
|
750
|
+
"opt": "--patch",
|
751
|
+
"arg": "in_file",
|
752
|
+
"description": ["If passed, it replaces the paths specified in the",
|
753
|
+
"patch."],
|
754
|
+
"source_url": "http://enve-omics.ce.gatech.edu/data/public_misc/patch_Silva_SSU_r115.txt"
|
755
|
+
},
|
756
|
+
{
|
757
|
+
"opt": "--seqinfo",
|
758
|
+
"arg": "out_file",
|
759
|
+
"description": ["If passed, it creates a CSV seq-info file",
|
760
|
+
"compatible with taxtastic."]
|
761
|
+
},
|
762
|
+
{
|
763
|
+
"opt": "--taxfile",
|
764
|
+
"arg": "out_file",
|
765
|
+
"description": "If passed, it creates a simple TSV taxonomy file."
|
766
|
+
},
|
767
|
+
{
|
768
|
+
"opt": "--ncbi",
|
769
|
+
"arg": "out_dir",
|
770
|
+
"description": ["If passed, output folder for the NCBI dump files",
|
771
|
+
"(e.g., taxdmp)."]
|
772
|
+
},
|
773
|
+
{
|
774
|
+
"opt": "--warns",
|
775
|
+
"description": "Verbously display warnings."
|
776
|
+
}
|
777
|
+
]
|
778
|
+
},
|
779
|
+
{
|
780
|
+
"task": "GFF.catsbj.pl",
|
781
|
+
"description": ["Generates a list of coordinates from a GFF table",
|
782
|
+
"concatenating the subject sequences."],
|
783
|
+
"help_arg": "-h",
|
784
|
+
"see_also": ["BlastTab.recplot2.R", "BlastTab.catsbj.pl"],
|
785
|
+
"options": [
|
786
|
+
{
|
787
|
+
"name": "Lim file",
|
788
|
+
"opt": "-L",
|
789
|
+
"arg": "out_file",
|
790
|
+
"description": ["An output file with the absolute coordinates of the",
|
791
|
+
"concatenated contigs. This is identical to the .lim file",
|
792
|
+
"generated by BlastTab.catsbj.pl."]
|
793
|
+
},
|
794
|
+
{
|
795
|
+
"name": "Inter-feature gaps",
|
796
|
+
"opt": "-i",
|
797
|
+
"description": ["Preserve exact coordinates and include",
|
798
|
+
"inter-feature windows as separate bins. By default, the",
|
799
|
+
"coordinates are set in the midpoint between features when",
|
800
|
+
"non-contiguous."]
|
801
|
+
},
|
802
|
+
{
|
803
|
+
"name": "Subset",
|
804
|
+
"opt": "-s",
|
805
|
+
"description": ["The FastA provided is to be treated as a subset of",
|
806
|
+
"the subject. By default, it expects all the contigs to be present",
|
807
|
+
"in the BLAST."]
|
808
|
+
},
|
809
|
+
{
|
810
|
+
"name": "Quiet",
|
811
|
+
"opt": "-q",
|
812
|
+
"description": "Run quietly."
|
813
|
+
},
|
814
|
+
{
|
815
|
+
"name": "Subject sequences",
|
816
|
+
"arg": "in_file",
|
817
|
+
"mandatory": true,
|
818
|
+
"description": "Subject sequences (contigs) in FastA format."
|
819
|
+
},
|
820
|
+
{
|
821
|
+
"name": "Features",
|
822
|
+
"arg": "in_file",
|
823
|
+
"mandatory": true,
|
824
|
+
"description": "Features to map in GFF."
|
825
|
+
}
|
826
|
+
]
|
827
|
+
},
|
828
|
+
{
|
829
|
+
"task": "Table.prefScore.R",
|
830
|
+
"description": ["Estimate preference score of species based on occupancy",
|
831
|
+
"in biased sample sets."],
|
832
|
+
"help_arg": "--help",
|
833
|
+
"requires": [ { "r_package": "optparse" } ],
|
834
|
+
"options": [
|
835
|
+
{
|
836
|
+
"name": "Occupancy matrix",
|
837
|
+
"opt": "--x",
|
838
|
+
"arg": "in_file",
|
839
|
+
"description": ["A tab-delimited table of presence/absence (1/0)",
|
840
|
+
"with species as rows and samples as columns."],
|
841
|
+
"mandatory": true
|
842
|
+
},
|
843
|
+
{
|
844
|
+
"name": "Sample set",
|
845
|
+
"opt": "--set",
|
846
|
+
"arg": "in_file",
|
847
|
+
"description": ["A list of sample names that constitute the test",
|
848
|
+
"set, one per line."],
|
849
|
+
"mandatory": true
|
850
|
+
},
|
851
|
+
{
|
852
|
+
"opt": "--ignore",
|
853
|
+
"arg": "in_file",
|
854
|
+
"description": ["A list of species to exclude from the analysis,",
|
855
|
+
"one per line."]
|
856
|
+
},
|
857
|
+
{
|
858
|
+
"name": "Significance threshold",
|
859
|
+
"opt": "--signif-thr",
|
860
|
+
"arg": "float",
|
861
|
+
"description": "Absolute value of the significance threshold."
|
862
|
+
},
|
863
|
+
{
|
864
|
+
"opt": "--col-above",
|
865
|
+
"arg": "string",
|
866
|
+
"description": "Color for points significantly above zero.",
|
867
|
+
"default": "#941100"
|
868
|
+
},
|
869
|
+
{
|
870
|
+
"opt": "--col-equal",
|
871
|
+
"arg": "string",
|
872
|
+
"description": ["Color for points not significantly different from",
|
873
|
+
"zero."],
|
874
|
+
"default": "#BDBDBD"
|
875
|
+
},
|
876
|
+
{
|
877
|
+
"opt": "--col-below",
|
878
|
+
"arg": "string",
|
879
|
+
"description": "Color for points significantly below zero.",
|
880
|
+
"default": "#2F5496"
|
881
|
+
},
|
882
|
+
{
|
883
|
+
"name": "Output preference scores",
|
884
|
+
"arg": "out_file",
|
885
|
+
"description": "Output raw-text file with preference scores.",
|
886
|
+
"mandatory": true
|
887
|
+
},
|
888
|
+
{
|
889
|
+
"name": "Graphical utput",
|
890
|
+
"arg": "out_file",
|
891
|
+
"description": "Output PDF file with preference scores plot."
|
892
|
+
},
|
893
|
+
{
|
894
|
+
"name": "Width",
|
895
|
+
"arg": "float",
|
896
|
+
"description": "Width of the plot in inches (7 by default)."
|
897
|
+
},
|
898
|
+
{
|
899
|
+
"name": "Height",
|
900
|
+
"arg": "float",
|
901
|
+
"description": "Height of the plot in inches (7 by default)."
|
902
|
+
}
|
903
|
+
]
|
904
|
+
}
|
905
|
+
]
|
906
|
+
}
|