Mercurial > repos > greg > ideas
changeset 11:6f486284731d draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 10 Aug 2017 13:13:15 -0400 |
| parents | 694d13d8b473 |
| children | 5b5733e09344 |
| files | ideas.xml |
| diffstat | 1 files changed, 9 insertions(+), 14 deletions(-) [+] |
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--- a/ideas.xml Thu Aug 10 12:58:33 2017 -0400 +++ b/ideas.xml Thu Aug 10 13:13:15 2017 -0400 @@ -9,13 +9,8 @@ </requirements> <command><![CDATA[ #import os -#set tmp_dir = 'tmp' -#set prep_output_dir = 'prep_output' -mkdir -p $tmp_dir && -mkdir -p $prep_output_dir && -echo "#############################################" && -echo $tmp_dir && -echo $output_dir && +mkdir -p tmp && +mkdir -p prep_output && ############################################## ## Create the config file and prepare the data ############################################## @@ -59,16 +54,16 @@ ## Build the R matrix from the prepMat output ############################################## #set r_matrix_input = None -#for f in $os.listdir($tmp_dir): +#for f in $os.listdir('tmp'): #if f.endswith('.bed.gz'): - #set r_matrix_input = $os.path.join($tmp_dir, $f) + #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_dir +-w 'tmp' ############################################## ## Run IDEAS on the R matrix ############################################## @@ -124,10 +119,10 @@ -maxerr $set_max_standard_dev_cond.max_standard_dev #end if -thread \${GALAXY_SLOTS:-4} --o $prep_output_dir -&& mv $prep_output_dir/*.state $output_state -&& mv $prep_output_dir/*.para $output_para -&& mv $prep_output_dir/*cluster $output_cluster +-o 'prep_output' +&& mv prep_output/*.state $output_state +&& mv prep_output/*.para $output_para +&& mv prep_output/*cluster $output_cluster ]]></command> <configfiles> <configfile name="build_config_file"><![CDATA[#for $input_items in $input_type_cond.input_repeat: