Mercurial > repos > mingchen0919 > one_command_liners
changeset 7:26a239300989 draft
initial tool
| author | mingchen0919 |
|---|---|
| date | Fri, 23 Feb 2018 11:23:30 -0500 |
| parents | 8c3b0ffa0d14 |
| children | ac0c560845dc |
| files | extract_fields.xml tool_template_render.R |
| diffstat | 2 files changed, 13 insertions(+), 11 deletions(-) [+] |
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--- a/extract_fields.xml Fri Feb 23 10:46:48 2018 -0500 +++ b/extract_fields.xml Fri Feb 23 11:23:30 2018 -0500 @@ -12,18 +12,19 @@ </stdio> <command><![CDATA[ Rscript '${__tool_directory__}/tool_template_render.R' -e $echo - -A $input_field_numbers - -B $input_txt - -O $output_txt -r $report -d $report.files_path -s $sink_message -t '${__tool_directory__}/tool_template.Rmd' + + -A $input_field_numbers + -B $input_file + -O $output_txt ]]></command> <inputs> <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/> - <param type="text" name="input_field_numbers" label="input field numbers" optional="False"/> - <param type="data" name="input_txt" label="Input text file" optional="False" format="txt"/> + <param type="data" name="input_file" label="Input file" optional="False"/> + <param type="text" name="input_field_numbers" label="Field numbers" optional="False"/> </inputs> <outputs> <data name="report" format="html" label="tool name report" hidden="false"/>
--- a/tool_template_render.R Fri Feb 23 10:46:48 2018 -0500 +++ b/tool_template_render.R Fri Feb 23 11:23:30 2018 -0500 @@ -2,16 +2,17 @@ sink(zz) sink(zz, type = "message") + # bring user inputs and command line arguments to R spec_matrix = as.matrix( data.frame(stringsAsFactors=FALSE, - long_flags = c("X_e", "X_A", "X_B", "X_O", "X_r", "X_d", "X_s", - "X_t"), + long_flags = c("X_e", "X_A", "X_B", "X_O", "X_r", "X_d", "X_s", + "X_t"), short_flags = c("e", "A", "B", "O", "r", "d", "s", "t"), - argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), - data_type_flags = c("character", "character", "character", "character", - "character", "character", "character", - "character") + argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), + data_type_flags = c("character", "character", "character", "character", + "character", "character", "character", + "character") ) ) opt = getopt::getopt(spec_matrix)