| Previous changeset 4:85166d75910b (2017-08-08) Next changeset 6:8cf3b1298508 (2017-08-15) |
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Commit message:
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 60ea96204588be4348bd5d7879d1eb0d73f487c7-dirty |
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modified:
i_adhore_configure.Rmd |
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| diff -r 85166d75910b -r dab02b629d48 i_adhore_configure.Rmd --- a/i_adhore_configure.Rmd Tue Aug 08 16:45:49 2017 -0400 +++ b/i_adhore_configure.Rmd Tue Aug 15 15:35:23 2017 -0400 |
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| @@ -47,17 +47,21 @@ # 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$blast_table, - 'output_path' = opt$i_adhore_configure_dir, + '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' = opt$level2only, + 'level_2_only' = tolower(opt$level2only), 'table_type' = opt$table_type, - 'multi_hypothesis_correction' = opt$multi_hypothesis_correction + 'multiple_hypothesis_correction' = opt$multi_hypothesis_correction ) df = data.frame(name = names(params), @@ -71,7 +75,7 @@ lines = c(unlist(g_analysis_files_list), ' ', paste0(df$name, '=', df$value), - 'CompareAligners') + 'compareAligners') fileConn = file('I_ADHORE_CONFIGURE_TXT') writeLines(lines, con = fileConn) ``` |