Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 83:21149dc86243

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"planemo upload"
author kkonganti
date Wed, 13 Jul 2022 16:49:53 -0400
parents 460fa12fd793
children de5b87ce9fe4
comparison
equal deleted inserted replaced
82:460fa12fd793 83:21149dc86243
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
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 $unpaired.name.endswith(('.fastq', '.fastq.gz')):
14 #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext) 14 #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext)
15 #else: 15 #else:
16 #set read1 = str($unpaired.name) 16 #set read1 = str($unpaired.name)
17 #end if 17 #end if
18 echo $unpaired.ext && ln -sf '$unpaired' './cpipes-input/$read1'; 18 ln -sf '$unpaired' './cpipes-input/$read1';
19 #end for 19 #end for
20 #elif (str($input_read_type_cond.input_read_type) == "paired"): 20 #elif (str($input_read_type_cond.input_read_type) == "paired"):
21 #for _, $pair in enumerate($input_read_type_cond.input_pair) 21 #for _, $pair in enumerate($input_read_type_cond.input_pair)
22 #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext) 22 #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext)
23 #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext) 23 #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext)