Mercurial > repos > iuc > bbtools_bbmap

comparison bbmap.xml @ 3:8157a81f511c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
author iuc
date Tue, 01 Feb 2022 23:01:08 +0000
parents e0ca2ec4f5d9
children 6d44c9f1a42b
comparison
equal deleted inserted replaced
2:e0ca2ec4f5d9 3:8157a81f511c
14 #set ref = $ref_source_cond.reference 14 #set ref = $ref_source_cond.reference
15 #end if 15 #end if
16 16
17 #if str($input_type_cond.input_type) in ['single', 'pair']: 17 #if str($input_type_cond.input_type) in ['single', 'pair']:
18 #set read1 = $input_type_cond.read1 18 #set read1 = $input_type_cond.read1
19 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
20 ## bbmap uses the file extension to determine the input format. 19 ## bbmap uses the file extension to determine the input format.
21 #set ext = $read1_identifier + '.fastq' 20 #set ext = '.fastq'
22 #if $read1.ext.endswith('.gz'): 21 #if $read1.ext.endswith('.gz'):
23 #set ext = $ext + '.gz' 22 #set ext = $ext + '.gz'
24 #end if 23 #end if
25 #set read1_file = $read1_identifier + $ext 24 #set read1_file = 'forward' + $ext
26 ln -s '${read1}' '${read1_file}' && 25 ln -s '${read1}' '${read1_file}' &&
27 #if str($input_type_cond.input_type) == 'pair': 26 #if str($input_type_cond.input_type) == 'pair':
28 #set read2 = $input_type_cond.read2 27 #set read2 = $input_type_cond.read2
29 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 28 #set read2_file = 'reverse' + $ext
30 #set read2_file = $read2_identifier + $ext
31 ln -s '${read2}' '${read2_file}' && 29 ln -s '${read2}' '${read2_file}' &&
32 #end if 30 #end if
33 #else: 31 #else:
34 #set read1 = $input_type_cond.reads_collection['forward'] 32 #set read1 = $input_type_cond.reads_collection['forward']
35 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name)) 33 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))