Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 77:d3ae287f740a

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 16:33:51 -0400
parents 0e35724b49f0
children 4ee79500795b
comparison
equal deleted inserted replaced
76:0e35724b49f0 77:d3ae287f740a
9 mkdir -p cpipes-input || exit 1; 9 mkdir -p cpipes-input || exit 1;
10 pwd_path=\$(pwd); 10 pwd_path=\$(pwd);
11 #if (str($input_read_type_cond.input_read_type) == "single_long"): 11 #if (str($input_read_type_cond.input_read_type) == "single_long"):
12 #for _, $unpaired in enumerate($input_read_type_cond.input): 12 #for _, $unpaired in enumerate($input_read_type_cond.input):
13 #if not $unpaired.ext.endswith(('.fastq', '.fastq.gz')): 13 #if not $unpaired.ext.endswith(('.fastq', '.fastq.gz')):
14 #set read_R1 = str($unpaired.name) + str($unpaired.ext) 14 #set read_R1 = str($unpaired.name) + str('.') + str($unpaired.ext)
15 #else: 15 #else:
16 #set read_R1 = str($unpaired.name) 16 #set read_R1 = str($unpaired.name)
17 #end if 17 #end if
18 echo $unpaired.ext
19 ln -sf '$unpaired' './cpipes-input/$read_R1'; 18 ln -sf '$unpaired' './cpipes-input/$read_R1';
20 #end for 19 #end for
21 #elif (str($input_read_type_cond.input_read_type) == "paired"): 20 #elif (str($input_read_type_cond.input_read_type) == "paired"):
22 #for _, $pair in enumerate($input_read_type_cond.input_pair) 21 #for _, $pair in enumerate($input_read_type_cond.input_pair)
23 #set read_R1 = str($pair.forward.name) + str($pair.forward.ext) 22 #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext)
24 #set read_R2 = str($pair.reverse.name) + str($pair.reverse.ext) 23 #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext)
25 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 24 ln -sf '$pair.forward' './cpipes-input/$read_R1';
26 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 25 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
27 #end for 26 #end for
28 #end if 27 #end if
29 $__tool_directory__/0.2.1/cpipes 28 $__tool_directory__/0.2.1/cpipes