diff i_adhore_configure.Rmd @ 0:9755ce6ac4d5 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/i_adhore_configure.Rmd	Tue Aug 08 12:53:57 2017 -0400
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+---
+title: 'i-adhore: generate i-adhore config file'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(echo = ECHO)
+```
+
+# Genomes and analysis files
+
+```{r}
+g_analysis_files_set = strsplit(opt$g_analysis_file, ';')[[1]]
+g_analysis_files_list = list()
+# for(i in g_analysis_files_set) {
+#   genome = strsplit(i, ':')[[1]][1]
+#   analysis_files = strsplit(i, ':')[[1]][2] %>% 
+#                       strsplit(',') %>% `[[`(1) %>% 
+#                       (function(x){
+#                         paste0(1:length(x),' ', x)
+#                       })
+#   g_analysis_files_list[[genome]] = analysis_files
+# }
+for(i in g_analysis_files_set) {
+  genome = strsplit(i, ':')[[1]][1]
+  analysis_files = strsplit(i, ':')[[1]][2] %>% 
+                      strsplit(',') %>% `[[`(1) %>% 
+                      laply(.fun = function(x){
+                        file_name = strsplit(x, '/')[[1]] %>% tail(1)
+                        file_name = strsplit(file_name, '\\.')[[1]][1]
+                        paste0(file_name, ' ', x)
+                      })
+  g_analysis_files_list[[genome]] = c(
+    'name' = paste0('genome=', strsplit(i, ':')[[1]][1]),
+    'analysis_files' = analysis_files
+  )
+  print(paste0('genome=', strsplit(i, ':')[[1]][1]))
+  print(analysis_files)
+}
+```
+
+# Other parameters
+
+```{r}
+params = c(
+  'blast table' = opt$blast_table,
+  'output_path' = opt$i_adhore_configure_dir,
+  'gap_size' = opt$gap_size,
+  'cluster_gap' = opt$cluster_gap,
+  'q_value' = opt$q_value,
+  'prob_cutoff' = opt$prob_cutoff,
+  'anchor_points' = opt$anchor_points,
+  'level_2_only' = opt$level2only,
+  'table_type' = opt$table_type,
+  'multi_hypothesis_correction' = opt$multi_hypothesis_correction
+)
+
+df = data.frame(name = names(params),
+                value = params)
+knitr::kable(df)
+```
+
+
+```{r echo=FALSE}
+# generate i_adhore_configure.txt file
+lines = c(unlist(g_analysis_files_list), 
+          ' ', 
+          paste0(df$name, '=', df$value), 
+          'CompareAligners')
+fileConn = file('I_ADHORE_CONFIGURE_TXT')
+writeLines(lines, con = fileConn)
+```
+
+