Mercurial > repos > greg > vsnp_sample_names
diff vsnp_sample_names.xml @ 1:895d18fcfebe draft
Uploaded
author | greg |
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date | Tue, 27 Oct 2020 18:21:55 +0000 |
parents | f75e2ac7b6cd |
children | a56648c94fd3 |
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--- a/vsnp_sample_names.xml Tue Apr 21 10:17:20 2020 -0400 +++ b/vsnp_sample_names.xml Tue Oct 27 18:21:55 2020 +0000 @@ -4,7 +4,7 @@ #import os #import re #set output_dir = 'output' -mkdir -p $output_dir +mkdir -p $output_dir && #if str($input_type_cond.input_type) == "single": ## We may have a single read or a pair, but in ## either case we want the same base file name. @@ -15,7 +15,7 @@ #if $sample_name.find("_") > 0: #set sample_name = $sample_name.split("_")[0] #end if - echo $sample_name > $output + && echo '$sample_name' > '$output' #else: #for $i in $input_type_cond.reads_collection: #set sample_name = $os.path.basename($i.element_identifier) @@ -23,7 +23,7 @@ #set sample_name = $sample_name.split(".")[0] #end if #set output_file = $os.path.join($output_dir, $sample_name) - && echo $sample_name > $output_file + && echo '$sample_name' > '$output_file' #end for #end if ]]></command>