Mercurial > repos > greg > vsnp_sample_names
comparison vsnp_sample_names.xml @ 1:895d18fcfebe draft
Uploaded
author | greg |
---|---|
date | Tue, 27 Oct 2020 18:21:55 +0000 |
parents | f75e2ac7b6cd |
children | a56648c94fd3 |
comparison
equal
deleted
inserted
replaced
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"> |