Mercurial > repos > greg > ideas
changeset 3:9874800487e6 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 10 Aug 2017 12:34:52 -0400 |
| parents | 7a77ec6342c1 |
| children | 445bafcf9a4b |
| files | ideas.xml |
| diffstat | 1 files changed, 20 insertions(+), 1 deletions(-) [+] |
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--- a/ideas.xml Thu Aug 10 12:34:42 2017 -0400 +++ b/ideas.xml Thu Aug 10 12:34:52 2017 -0400 @@ -8,8 +8,11 @@ <requirement type="package" version="1.2.0">ideas</requirement> </requirements> <command><![CDATA[ +#import os mkdir -p tmp && +############################################## ## Create the config file and prepare the data +############################################## #set input_type = $input_type_cond.input_type cp '$build_config_file' 'config_file.txt' && prepMat @@ -46,7 +49,23 @@ #if str($standardize_datasets) == 'yes': -norm #end if -## Run IDEAS on the prepared data +############################################## +## Build the R matrix from the prepMat output +############################################## +#set r_matrix_input = None +#for f in $os.listdir(tmp): + #if f.endswith('.bed.gz'): + #set r_matrix_input = $os.path.join(tmp, f) + #end if +#end for +#assert $r_matrix_input is not None and $os.path.getsize($r_matrix_input) > 0, "Output file from prepMat is missing or empty." +&& Rscript '$__tool_directory__/build_matrix.R' +-i $r_matrix_input +-o '%s.input' % $f +-w 'tmp' +############################################## +## Run IDEAS on the R matrix +############################################## && mkdir -p output && ideas '$build_config_file'