Mercurial > repos > siwaa > redelac_stics_g
changeset 3:e344100f3354 draft
"planemo upload for repository https://forgemia.inra.fr/redelac commit ff64e62033c2485113100d60c38be73e59ef119c"
| author | siwaa | 
|---|---|
| date | Thu, 29 Jun 2023 10:50:58 +0000 | 
| parents | c60c25773642 | 
| children | af7d9ca55205 | 
| files | redelacSticsInputGenerator.R redelacSticsInputGenerator.xml test-data/input/Ini.csv test-data/input/StationExp.csv test-data/input/Tec.csv test-data/input/USMsExp.csv test-data/input/rot1_2.zip | 
| diffstat | 7 files changed, 11 insertions(+), 1606 deletions(-) [+] | 
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--- a/redelacSticsInputGenerator.R Mon Jun 19 17:25:39 2023 +0000 +++ b/redelacSticsInputGenerator.R Thu Jun 29 10:50:58 2023 +0000 @@ -7,11 +7,6 @@ txt_path <- paste0(getwd(), "/WS/txt_files") dir.create(txt_path,recursive = T) -gen_usms_xml2txt(javastics = javastics_path, - workspace = workspace, - out_dir = txt_path, - check = FALSE) - USMsFile <- "USMs.csv" TecFile <- "Tec.csv" IniFile <- "Ini.csv" @@ -25,8 +20,10 @@ gen_usms_xml(file = file.path(workspace, "usms.xml"), param_df = usms_param) # Tec files -tec_param <- read_params_table(file.path(workspace, TecFile)) -gen_tec_xml(param_table = tec_param, out_path = workspace) +tec_param <- read_params_table(file.path(workspace, TecFile)) %>% + select(!c(annee, date_min, date_max, Date_res_1, Date_res_2, Type_res_1, Type_res_2, Date_trav_1, Date_trav_2, Date_trav_3, Type_trav_1, Type_trav_2 ,Type_trav_3, plante_sem, date_sem, starts_with("nom_vari"), date_ferti_1, date_ferti_2, date_ferti_3, type_eng_1, type_eng_2, type_eng_3, date_rec, date_des, juleclair, nbinfloecl)) +gen_tec_xml(param_df = tec_param, out_dir = workspace) +# select(!c(annee, date_min, date_max, Date_res_1, Date_res_2, Type_res_1, Type_res_2, Date_trav_1, Date_trav_2, Date_trav_3, Type_trav_1, Type_trav_2 ,Type_trav_3, plante_sem, date_sem) # Ini files ini_param <- read_params_table(file.path(workspace, IniFile)) @@ -43,10 +40,9 @@ ### Generate txt files into individual folders # generate text files -gen_usms_xml2txt(javastics = javastics_path, - workspace = workspace, +gen_usms_xml2txt(javastics = javastics_path, + workspace = workspace, out_dir = txt_path, verbose = TRUE, - usm = list_usms, - check=FALSE) #je mets l'option a FALSE car sinon j'ai soit disant des fichiers climatiques manquants du type 14050.198,14050.199,14050.2 (pas de lecture des z?ros) + usm = list_usms) \ No newline at end of file
--- a/redelacSticsInputGenerator.xml Mon Jun 19 17:25:39 2023 +0000 +++ b/redelacSticsInputGenerator.xml Thu Jun 29 10:50:58 2023 +0000 @@ -1,7 +1,7 @@ -<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.0"> +<tool id="redelacSticsInputGenerator" name="redelacSticsInputGenerator" version="1.0.1"> <description>to run generate Stics Inputs for REDELAC</description> <requirements> - <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics:10.0.0</container> + <container type="singularity">docker://registry.forgemia.inra.fr/quaysofthestics/sticsquays/rstudio_stics_test:10.0.0</container> </requirements> <command detect_errors="aggressive"> <