Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 60:5c0901d0d8a8

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 12:56:29 -0400
parents a8d6f5950fbf
children 29fec32b8f47
comparison
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59:a8d6f5950fbf 60:5c0901d0d8a8
18 #set $read_R1 = os.path.basename($input_read_type_cond.input_pair[$key]['forward']) 18 #set $read_R1 = os.path.basename($input_read_type_cond.input_pair[$key]['forward'])
19 #set $read_R2 = os.path.basename($input_read_type_cond.input_pair[$key]['reverse']) 19 #set $read_R2 = os.path.basename($input_read_type_cond.input_pair[$key]['reverse'])
20 ln -sf '$input_read_type_cond.input_pair[$key]['forward']' './cpipes-input/$read_R1'; 20 ln -sf '$input_read_type_cond.input_pair[$key]['forward']' './cpipes-input/$read_R1';
21 ln -sf '$input_read_type_cond.input_pair[$key]['reverse']' './cpipes-input/$read_R2'; 21 ln -sf '$input_read_type_cond.input_pair[$key]['reverse']' './cpipes-input/$read_R2';
22 #end for 22 #end for
23 #endif 23 #end if
24 $__tool_directory__/0.2.1/cpipes 24 $__tool_directory__/0.2.1/cpipes
25 --pipeline $input_read_type_cond.pipeline 25 --pipeline $input_read_type_cond.pipeline
26 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 26 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
27 --fq_single_end true 27 --fq_single_end true
28 --flye_genome_size '${genome_size}' 28 --flye_genome_size '${genome_size}'