Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 26:2fb6c7a719d4

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 13:21:05 -0400
parents b9cd7722d51b
children ec561fc0e030
comparison
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25:b9cd7722d51b 26:2fb6c7a719d4
10 #for $key in $input.keys() 10 #for $key in $input.keys()
11 ln -sf '$input[$key]' './cpipes-input/$key'; 11 ln -sf '$input[$key]' './cpipes-input/$key';
12 #end for 12 #end for
13 pwd_path=\$(pwd); 13 pwd_path=\$(pwd);
14 $__tool_directory__/0.2.1/cpipes 14 $__tool_directory__/0.2.1/cpipes
15 --pipeline $pipeline
15 #if ($pipeline == "centriflaken"): 16 #if ($pipeline == "centriflaken"):
16 --pipeline $pipeline
17 --fq_single_end true 17 --fq_single_end true
18 #elif ($pipeline == "centriflaken_hy"): 18 #elif ($pipeline == "centriflaken_hy"):
19 --pipeline $pipeline
20 #if ($reads_lib_layout == "single"): 19 #if ($reads_lib_layout == "single"):
21 --fq_single_end true 20 --fq_single_end true
22 #else: 21 #else:
23 --fq_single_end false 22 --fq_single_end false
24 #end if 23 #end if