Mercurial > repos > greg > vsnp_statistics

comparison vsnp_statistics.xml @ 18:076069733de7 draft

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author greg
date Wed, 04 Aug 2021 13:27:17 +0000
parents 44b07199be73
children d4ef7003c539
comparison
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17:932e517b5779 18:076069733de7
21 #set read2 = $input_type_cond.read2 21 #set read2 = $input_type_cond.read2
22 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 22 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
23 ln -s '${read2}' '${read2_identifier}' && 23 ln -s '${read2}' '${read2_identifier}' &&
24 #end if 24 #end if
25 #else: 25 #else:
26 #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.reads_collection.element_identifier))
26 #set read1 = $input_type_cond.reads_collection.forward 27 #set read1 = $input_type_cond.reads_collection.forward
27 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) 28 #set read1_identifier = $identifier + '_R1'
28 ln -s '${read1}' '${read1_identifier}' && 29 ln -s '${read1}' '${read1_identifier}' &&
29 #set read2 = $input_type_cond.reads_collection.reverse 30 #set read2 = $input_type_cond.reads_collection.reverse
30 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 31 #set read2_identifier = $identifier + '_R2'
31 ln -s '${read2}' '${read2_identifier}' && 32 ln -s '${read2}' '${read2_identifier}' &&
32 #end if 33 #end if
33 34
34 python '$__tool_directory__/vsnp_statistics.py' 35 python '$__tool_directory__/vsnp_statistics.py'
35 --read1 '${read1_identifier}' 36 --read1 '${read1_identifier}'