elynx-tools 0.7.2.1 → 0.7.2.2
raw patch · 3 files changed
+30/−27 lines, 3 filesdep ~optparse-applicative
Dependency ranges changed: optparse-applicative
Files
- README.md +11/−8
- elynx-tools.cabal +3/−3
- src/ELynx/Tools/Options.hs +16/−16
README.md view
@@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.7.2.0.+Version: 0.7.2.1. Reproducible evolution made easy. <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -73,9 +73,9 @@ # OR: stack exec slynx -- --help # OR: slynx --help - ELynx Suite version 0.7.2.0.+ ELynx Suite version 0.7.2.1. Developed by Dominik Schrempf.- Compiled on May 3, 2023, at 13:18 pm, UTC.+ Compiled on June 15, 2023, at 19:54 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND@@ -143,17 +143,17 @@ # OR: stack exec slynx -- simulate --help # OR: slynx simulate --help - Up to date- ELynx Suite version 0.7.0.0.+ ELynx Suite version 0.7.2.1. Developed by Dominik Schrempf.- Compiled on July 10, 2022, at 08:48 am, UTC.+ Compiled on June 15, 2023, at 19:54 pm, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]- [-m|--mixture-model MODEL] [-e|--edm-file NAME]- [-p|--siteprofile-files NAMES]+ [-m|--mixture-model MODEL] [-n|--global-normalization]+ [-e|--edm-file NAME] [-p|--siteprofile-files NAMES] [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"] [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"] (-l|--length NUMBER) [-S|--seed INT]+ Simulate multi sequence alignments. Available options:@@ -166,6 +166,9 @@ option) -m,--mixture-model MODEL Set the phylogenetic mixture model; available models are shown below (mutually exclusive with -s option)+ -n,--global-normalization+ Normalize mixture model globally (one normalization+ constant for all components) -e,--edm-file NAME Empirical distribution model file NAME in Phylobayes format -p,--siteprofile-files NAMES
elynx-tools.cabal view
@@ -1,6 +1,6 @@ cabal-version: 3.0 name: elynx-tools-version: 0.7.2.1+version: 0.7.2.2 synopsis: Tools for ELynx description: Please see the README on GitHub at <https://github.com/dschrempf/elynx>.@@ -41,13 +41,13 @@ build-depends: , aeson , attoparsec- , base >=4.7 && <5+ , base >=4.7 && <5 , base16-bytestring , bytestring , cryptohash-sha256 , directory , hmatrix- , optparse-applicative+ , optparse-applicative >=0.18.1.0 && <1.0 , random , template-haskell , time
src/ELynx/Tools/Options.hs view
@@ -224,26 +224,26 @@ -- Fill a string so that it becomes a paragraph with line breaks. Useful for -- descriptions, headers and footers. fillParagraph :: String -> Doc-fillParagraph = fillSep . map text . words+fillParagraph = fillSep . map pretty . words -- | Global ELynx footer. elynxFooter :: [Doc] elynxFooter =- [ empty,- text "ELynx",- text "-----",+ [ mempty,+ pretty "ELynx",+ pretty "-----", fillParagraph "A Haskell library and tool set for computational biology. The goal of ELynx is reproducible research. Evolutionary sequences and phylogenetic trees can be read, viewed, modified and simulated. The command line with all arguments is logged consistently, and automatically. Data integrity is verified using SHA256 sums so that validation of past analyses is possible without the need to recompute the result.",- empty,- fill 9 (text "slynx")- <+> text "Analyze, modify, and simulate evolutionary sequences.",- fill 9 (text "tlynx")- <+> text "Analyze, modify, and simulate phylogenetic trees.",- fill 9 (text "elynx") <+> text "Validate and redo past analyses.",- empty,- text "Get help for commands:",- text " slynx --help",- empty,- text "Get help for sub commands:",- text " slynx examine --help"+ mempty,+ fill 9 (pretty "slynx")+ <+> pretty "Analyze, modify, and simulate evolutionary sequences.",+ fill 9 (pretty "tlynx")+ <+> pretty "Analyze, modify, and simulate phylogenetic trees.",+ fill 9 (pretty "elynx") <+> pretty "Validate and redo past analyses.",+ mempty,+ pretty "Get help for commands:",+ pretty " slynx --help",+ mempty,+ pretty "Get help for sub commands:",+ pretty " slynx examine --help" ]