Mercurial > repos > mingchen0919 > dynamic_tool_test

annotate helper.R @ 0:b49e227ec738 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
author mingchen0919
date Wed, 21 Mar 2018 17:26:27 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
1 #' \code{getopt_specification_matrix} returns a getopt specification matrix.
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
2 #'
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
3 #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
4 #' The first column are short flags, the second column are argument masks, the third column
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
5 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
6 #' @param gtg_name the name of a running GTG.
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
7 getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) {
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
8 df = read.csv(paste0(tool_dir, specification_file),
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
9 header = TRUE, stringsAsFactors = FALSE)
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
10 # check if there are duplicated short flags
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
11 short_flags = df[, 1]
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
12 if (length(unique(short_flags)) < length(short_flags)) {
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
13 cat('----Duplicated short flags found ----\n')
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
14 cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
15 stop('Duplicated short flags are not allowed.')
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
16 }
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
17
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
18 # use short flags to generate long flags
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
19 long_flags = paste0('X_', df[, 1])
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
20
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
21 # specification matrix
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
22 df2 = data.frame(long_flags = long_flags,
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
23 short_flags = df[, 1],
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
24 argument_mask = df[, 2],
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
25 data_type = df[, 3])
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
26
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
27 as.matrix(df2)
b49e227ec738 planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190
mingchen0919
parents:
diff changeset
28 }