Mercurial > repos > kkonganti > cfsan_centriflaken

comparison cfsan_centriflaken.xml @ 96:ef0b422978fd

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Mon, 25 Jul 2022 12:57:06 -0400
parents ca861be31596
children ce6d9548fe89
comparison
equal deleted inserted replaced
95:aefcf9bbaee5 96:ef0b422978fd
11 #import re 11 #import re
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 _, $unpaired in enumerate($input_read_type_cond.input): 13 #for _, $unpaired in enumerate($input_read_type_cond.input):
14 #set read1 = str($unpaired.name) 14 #set read1 = str($unpaired.name)
15 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')): 15 #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
16 #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext) 16 #set read1_ext = re.sub('fastqsanger', 'fastq', str($unpaired.ext))
17 #set read1 = str($unpaired.name) + str('.') + $read1_ext
17 #end if 18 #end if
18 ln -sf '$unpaired' './cpipes-input/$read1'; 19 ln -sf '$unpaired' './cpipes-input/$read1';
19 #end for 20 #end for
20 #elif (str($input_read_type_cond.input_read_type) == "paired"): 21 #elif (str($input_read_type_cond.input_read_type) == "paired"):
21 #for _, $pair in enumerate($input_read_type_cond.input_pair) 22 #for _, $pair in enumerate($input_read_type_cond.input_pair)
22 #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name)) 23 #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name))
23 #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name)) 24 #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name))
25 #set read_R1_ext = re.sub('fastqsanger', 'fastq', str($pair.forward.ext))
26 #set read_R2_ext = re.sub('fastqsanger', 'fastq', str($pair.reverse.ext))
24 #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')): 27 #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
25 #set read_R1 = $read_R1 + str('.') + str($pair.forward.ext) 28 #set read_R1 = $read_R1 + str('.') + $read_R1_ext
26 #end if 29 #end if
27 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')): 30 #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
28 #set read_R2 = $read_R2 + str('.') + str($pair.reverse.ext) 31 #set read_R2 = $read_R2 + str('.') + $read_R2_ext
29 #end if 32 #end if
30 ln -sf '$pair.forward' './cpipes-input/$read_R1'; 33 ln -sf '$pair.forward' './cpipes-input/$read_R1';
31 ln -sf '$pair.reverse' './cpipes-input/$read_R2'; 34 ln -sf '$pair.reverse' './cpipes-input/$read_R2';
32 #end for 35 #end for
33 #end if 36 #end if