comparison i_adhore_configure.Rmd @ 5:dab02b629d48 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 60ea96204588be4348bd5d7879d1eb0d73f487c7-dirty

4:85166d75910b

```

# 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)
```

5:dab02b629d48

```

# Other parameters

```{r}
data_dir = gsub('dataset_.*dat', '', opt$blast_table)
output_dir = tail(strsplit(opt$i_adhore_configure_dir, '/')[[1]], 1)
output_path = paste(data_dir, output_dir, sep = '')
                  
params = c(
  'blast_table' = opt$blast_table,
  'output_path' = output_path,
  'gap_size' = opt$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' = tolower(opt$level2only),
  'table_type' = opt$table_type,
  'multiple_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)
```