Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 69:905def920829

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 14:10:46 -0400
parents 44d4e4078aaa
children 4e72dfe54475
comparison
equal deleted inserted replaced
68:44d4e4078aaa 69:905def920829
12 #if (str($input_read_type_cond.input_read_type) == "single_long"): 12 #if (str($input_read_type_cond.input_read_type) == "single_long"):
13 #for $key in $input_read_type_cond.input.keys() 13 #for $key in $input_read_type_cond.input.keys()
14 ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key'; 14 ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key';
15 #end for 15 #end for
16 #elif (str($input_read_type_cond.input_read_type) == "paired"): 16 #elif (str($input_read_type_cond.input_read_type) == "paired"):
17 #for $key in $input_read_type_cond.input_pair.keys() 17 #for _, $pair in enumerate($input_read_type_cond.input_pair)
18 #set $read_R1 = os.path.basename(str($input_read_type_cond.input_pair[$key]['forward'])) 18 #set $read_R1 = os.path.basename(str(${pair.forward}))
19 #set $read_R2 = os.path.basename(str($input_read_type_cond.input_pair[$key]['reverse'])) 19 #set $read_R2 = os.path.basename(str(${pair.reverse}))
20 ln -sf "$input_read_type_cond.input_pair[$key]['forward']" './cpipes-input/$key'; 20 ln -sf '${pair.forward}' './cpipes-input/${read_R1.name}';
21 ln -sf "$input_read_type_cond.input_pair[$key]['reverse']" './cpipes-input/$key'; 21 ln -sf '${pair.reverse}' './cpipes-input/${read_R2.name}';
22 #end for 22 #end for
23 #end if 23 #end if
24 $__tool_directory__/0.2.1/cpipes 24 $__tool_directory__/0.2.1/cpipes
25 --pipeline $input_read_type_cond.pipeline_cond.pipeline 25 --pipeline $input_read_type_cond.pipeline_cond.pipeline
26 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"): 26 #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):