# HG changeset patch # User dfornika # Date 1528306056 14400 # Node ID 97c29398c1c57ce4ddf269f2f3f13da500592605 # Parent 1f765046e008dc372f57a0a7f1419231770b8358 planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 141a199133b54e86a7501d6dfc68e9d77c7150ea diff -r 1f765046e008 -r 97c29398c1c5 data_managers/data_manager_conf.xml --- a/data_managers/data_manager_conf.xml Thu May 31 13:30:07 2018 -0400 +++ b/data_managers/data_manager_conf.xml Wed Jun 06 13:27:36 2018 -0400 @@ -1,6 +1,6 @@ - + @@ -15,7 +15,7 @@ - + @@ -30,7 +30,7 @@ - + @@ -45,7 +45,7 @@ - + diff -r 1f765046e008 -r 97c29398c1c5 data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml --- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml Thu May 31 13:30:07 2018 -0400 +++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml Wed Jun 06 13:27:36 2018 -0400 @@ -1,7 +1,7 @@ - + - mentalist + mentalist - + - mentalist + mentalist - + - mentalist + mentalist - + - mentalist + mentalist + - mentalist + mentalist + r-base @@ -15,16 +15,16 @@ - - + + - - + + - - + + \n") +} + +main <- function(args) { + if(is.na(args[1])){ + usage() + return() + } + suppressMessages(library(phangorn)) + + distance_matrix <- read.csv(args[1], row.names=1, sep="\t") + upgma_tree <- upgma(distance_matrix) + newick_tree <- write.tree(upgma_tree) + cat(newick_tree, '\n') +} + +if(!interactive()) { + main(args) +} diff -r 1f765046e008 -r 97c29398c1c5 tools/mentalist_tree/mentalist_tree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mentalist_tree/mentalist_tree.xml Wed Jun 06 13:27:36 2018 -0400 @@ -0,0 +1,36 @@ + + + r-base + r-phangorn + + '${output}' + ]]> + + + + + + + + + + + + + + + + + + + + + + ]]> + + +