Mercurial > repos > greg > vsnp_sample_names
comparison vsnp_sample_names.xml @ 1:895d18fcfebe draft
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| author | greg |
|---|---|
| date | Tue, 27 Oct 2020 18:21:55 +0000 |
| parents | f75e2ac7b6cd |
| children | a56648c94fd3 |
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| 0:f75e2ac7b6cd | 1:895d18fcfebe |
|---|---|
| 2 <description></description> | 2 <description></description> |
| 3 <command detect_errors="exit_code"><![CDATA[ | 3 <command detect_errors="exit_code"><![CDATA[ |
| 4 #import os | 4 #import os |
| 5 #import re | 5 #import re |
| 6 #set output_dir = 'output' | 6 #set output_dir = 'output' |
| 7 mkdir -p $output_dir | 7 mkdir -p $output_dir && |
| 8 #if str($input_type_cond.input_type) == "single": | 8 #if str($input_type_cond.input_type) == "single": |
| 9 ## We may have a single read or a pair, but in | 9 ## We may have a single read or a pair, but in |
| 10 ## either case we want the same base file name. | 10 ## either case we want the same base file name. |
| 11 #set sample_name = $os.path.basename($input_type_cond.read.element_identifier) | 11 #set sample_name = $os.path.basename($input_type_cond.read.element_identifier) |
| 12 #if $sample_name.find(".") > 0: | 12 #if $sample_name.find(".") > 0: |
| 13 #set sample_name = $sample_name.split(".")[0] | 13 #set sample_name = $sample_name.split(".")[0] |
| 14 #end if | 14 #end if |
| 15 #if $sample_name.find("_") > 0: | 15 #if $sample_name.find("_") > 0: |
| 16 #set sample_name = $sample_name.split("_")[0] | 16 #set sample_name = $sample_name.split("_")[0] |
| 17 #end if | 17 #end if |
| 18 echo $sample_name > $output | 18 && echo '$sample_name' > '$output' |
| 19 #else: | 19 #else: |
| 20 #for $i in $input_type_cond.reads_collection: | 20 #for $i in $input_type_cond.reads_collection: |
| 21 #set sample_name = $os.path.basename($i.element_identifier) | 21 #set sample_name = $os.path.basename($i.element_identifier) |
| 22 #if $sample_name.find(".") > 0: | 22 #if $sample_name.find(".") > 0: |
| 23 #set sample_name = $sample_name.split(".")[0] | 23 #set sample_name = $sample_name.split(".")[0] |
| 24 #end if | 24 #end if |
| 25 #set output_file = $os.path.join($output_dir, $sample_name) | 25 #set output_file = $os.path.join($output_dir, $sample_name) |
| 26 && echo $sample_name > $output_file | 26 && echo '$sample_name' > '$output_file' |
| 27 #end for | 27 #end for |
| 28 #end if | 28 #end if |
| 29 ]]></command> | 29 ]]></command> |
| 30 <inputs> | 30 <inputs> |
| 31 <conditional name="input_type_cond"> | 31 <conditional name="input_type_cond"> |