Merge pull request #39 from phac-nml/cmdline

Move Cmdline branch to master

.gitignore

@@ -1,3 +1,4 @@
+.Rproj
 .Rproj.user
 .Rhistory
 .RData

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "extdata"]
+	path = inst/extdata
+	url = https://github.com/phac-nml/wade-data.git

DESCRIPTION

@@ -1,23 +1,24 @@
 Package: wade
 Title: Executes molecular typing on contig assemblies
-Version: 0.1.0
-Authors@R: person("Justin", "Band", email = "[email protected]", role = c("aut", "cre"))
+Version: 0.2.6
+Authors@R: c(person("Adrian", "Zetner", email = "[email protected]", role = c("aut", "cre")),
+              person("Walter", "Demczuk", email = "[email protected]", role = c("aut")),
+              person("Justin", "Band", email = "[email protected]", role = c("aut")))
 Description: Creates an output_profile.csv of molecular typing results.
-Depends: R (>= 3.5.2)
-License: NML/PHAC
+Depends: R (>= 3.6)
+License: Apache License 2.0
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1.9000
+RoxygenNote: 7.0.0
+biocViews:
+    Biostrings
 Imports:
-    devtools,
     dplyr,
-    GalaxyConnector,
     here,
     purrr,
-    shiny,
-    shinydashboard,
-    shinyFiles,
-    shinyWidgets,
-    stringr
+    magrittr,
+    stringr,
+    optparse,
+    Biostrings
 Suggests: 
-	testthat
+	testthat

NAMESPACE

@@ -1,17 +1,32 @@
 # Generated by roxygen2: do not edit by hand
 
-export(Index_pipeline)
 export(PneumoCaT_pipeline)
+export(blast)
 export(database_pipeline)
 export(emm)
 export(general_mlst_pipeline)
-export(get_labware_dataframe)
-export(get_samples)
-export(labware_gas_amr)
-export(labware_gas_toxins)
 export(labware_gono_amr)
 export(master_blastr)
-export(metrics)
 export(rna_23s)
-export(server)
-export(ui)
+import(Biostrings)
+import(here)
+import(magrittr)
+import(utils)
+importFrom(dplyr,arrange)
+importFrom(dplyr,bind_cols)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
+importFrom(dplyr,select)
+importFrom(purrr,is_empty)
+importFrom(purrr,map)
+importFrom(purrr,map2_df)
+importFrom(purrr,map_df)
+importFrom(purrr,map_dfr)
+importFrom(purrr,pmap)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_length)
+importFrom(stringr,str_remove)
+importFrom(stringr,str_replace_all)
+importFrom(stringr,str_split)
+importFrom(stringr,str_sub)