diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..6afd8fa --- /dev/null +++ b/.gitignore @@ -0,0 +1,10 @@ +tool_test_output.html +tool_test_output.json +.DS_Store +.tox +*.pyc +.*.log +.idea/* +.git/* +.Rhistory +.RData diff --git a/tools/Xlsxtotabular/test-data/dummy.tsv b/tools/Xlsxtotabular/test-data/dummy.tsv new file mode 100644 index 0000000..52fd3e7 --- /dev/null +++ b/tools/Xlsxtotabular/test-data/dummy.tsv @@ -0,0 +1,43 @@ +"sample" "nb_mutations" "TMB" "cohort" +"PAMXZY" 2 "0.0606770343493" "TARGET" +"PAMYMA" 1 "0.0303385171746" "TARGET" +"PANVPB" 1 "0.0303385171746" "TARGET" +"PANZLR" 2 "0.0606770343493" "TARGET" +"PARBTV" 1 "0.0303385171746" "TARGET" +"PARHRS" 0 "0.0" "TARGET" +"PARLSL" 3 "0.0910155515239" "TARGET" +"PARNAW" 0 "0.0" "TARGET" +"PARXYR" 2 "0.0606770343493" "TARGET" +"PARZIA" 1 "0.0303385171746" "TARGET" +"PASDKZ" 1 "0.0303385171746" "TARGET" +"PASDXR" 1 "0.0303385171746" "TARGET" +"PASFHK" 2 "0.0606770343493" "TARGET" +"PASFJJ" 3 "0.0910155515239" "TARGET" +"PASFLG" 1 "0.0303385171746" "TARGET" +"PASIGA" 1 "0.0303385171746" "TARGET" +"PASLZE" 1 "0.0303385171746" "TARGET" +"PASNKZ" 1 "0.0303385171746" "TARGET" +"PASSLT" 0 "0.0" "TARGET" +"PASTZK" 6 "0.182031103048" "TARGET" +"PASVJS" 2 "0.0606770343493" "TARGET" +"PASYEJ" 1 "0.0303385171746" "TARGET" +"PASYWA" 3 "0.0910155515239" "TARGET" +"PATAIJ" 0 "0.0" "TARGET" +"PATHIU" 1 "0.0303385171746" "TARGET" +"PATISD" 1 "0.0303385171746" "TARGET" +"PATJMY" 1 "0.0303385171746" "TARGET" +"PATKBK" 3 "0.0910155515239" "TARGET" +"PATKKJ" 7 "0.212369620222" "TARGET" +"PATKWH" 2 "0.0606770343493" "TARGET" +"cBOURI" 549 "16.6558459289" "CONECT" +"c29007" 57 "1.72929547895" "CONECT" +"c21006" 152 "4.61145461054" "CONECT" +"c20017" 41 "1.24387920416" "CONECT" +"c17009" 140 "4.24739240445" "CONECT" +"c13026" 38 "1.15286365264" "CONECT" +"c13009" 87 "2.63945099419" "CONECT" +"c08006" 171 "5.18788643686" "CONECT" +"c05007" 80 "2.42708137397" "CONECT" +"c01044" 58 "1.75963399613" "CONECT" +"c01021" 357 "10.8308506313" "CONECT" +"c01002" 75 "2.2753887881" "CONECT" diff --git a/tools/Xlsxtotabular/test-data/dummy.xlsx b/tools/Xlsxtotabular/test-data/dummy.xlsx new file mode 100644 index 0000000..0070384 Binary files /dev/null and b/tools/Xlsxtotabular/test-data/dummy.xlsx differ diff --git a/tools/Xlsxtotabular/test-data/out.tabular b/tools/Xlsxtotabular/test-data/out.tabular new file mode 100644 index 0000000..b377ad7 --- /dev/null +++ b/tools/Xlsxtotabular/test-data/out.tabular @@ -0,0 +1 @@ +"french museum" diff --git a/tools/Xlsxtotabular/xls2tab.R b/tools/Xlsxtotabular/xls2tab.R index cabe862..b964b4a 100644 --- a/tools/Xlsxtotabular/xls2tab.R +++ b/tools/Xlsxtotabular/xls2tab.R @@ -1,8 +1,9 @@ #!/usr/bin/env Rscript -#Read xls/xlsx sheets - return tabular -library(readxl) -args = commandArgs(trailingOnly=TRUE) +# Read xls/xlsx sheets - return tabular + +library(readxl) -sheet<-read_excel(args[1],sheet=args[2]) -write.table(sheet,"out.tabular",sep="\t",row.names=FALSE) \ No newline at end of file +args = commandArgs(trailingOnly = TRUE) +sheet <- read_excel(args[1],sheet = args[2]) +write.table(sheet,"out.tabular", sep = "\t", row.names = FALSE) diff --git a/tools/Xlsxtotabular/xls2tab.xml b/tools/Xlsxtotabular/xls2tab.xml index ef78eb4..b1eaffb 100644 --- a/tools/Xlsxtotabular/xls2tab.xml +++ b/tools/Xlsxtotabular/xls2tab.xml @@ -1,7 +1,6 @@ - + - R - r-readxl + r-readxl @@ -24,6 +23,12 @@ + + + + + + @@ -45,8 +50,8 @@ Output tabular **Arguments** -Input: xls/xlsx file. -Excel sheet name: données in situ +Input: xls/xlsx file. (xls not tested) +Excel sheet name: 'données in situ' (for instance)