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comparison vsnp_determine_ref_from_data.xml @ 3:6116deacb2c7 draft

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author greg
date Mon, 23 Nov 2020 21:42:34 +0000
parents ee6166a3edd8
children 36bdf8b439ed
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2:ee6166a3edd8 3:6116deacb2c7
32 #if $read1.is_of_type('fastqsanger.gz') and $read2.is_of_type('fastqsanger.gz'): 32 #if $read1.is_of_type('fastqsanger.gz') and $read2.is_of_type('fastqsanger.gz'):
33 #set gzipped = 'true' 33 #set gzipped = 'true'
34 #end if 34 #end if
35 #end if 35 #end if
36 #else: 36 #else:
37 #set collection_type = $input_type_cond.collection_type_cond.collection_type
37 #for $i in $input_type_cond.collection_type_cond.reads_collection: 38 #for $i in $input_type_cond.collection_type_cond.reads_collection:
38 #if $i.is_of_type('fastqsanger.gz'): 39 #if $i.is_of_type('fastqsanger.gz'):
39 #set gzipped = 'true' 40 #set gzipped = 'true'
40 #end if 41 #end if
41 #set filename = $i.file_name 42 #set filename = $i.file_name
42 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) 43 #if str($collection_type) == 'single_reads':
44 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
45 #else:
46 ## Galaxy builds lists of pairs as nested lists with elements
47 ## named forward and reverse. When flattened, these lists
48 ## will work as inputs to the Parse parameter value expression
49 ## tool in workflows. However, the output list created by the
50 ## expression tool will not function correctly with the bwa_mem
51 ## mapper. Naming the identifier as follows is a solution.
52 #set identifier = re.sub('[^\s\w\-]', '_', str($i.name))
53 #end if
43 ln -s '$filename' '$input_reads_dir/$identifier' && 54 ln -s '$filename' '$input_reads_dir/$identifier' &&
44 #end for 55 #end for
45 #end if 56 #end if
46 python '$__tool_directory__/vsnp_determine_ref_from_data.py' 57 python '$__tool_directory__/vsnp_determine_ref_from_data.py'
47 #if str($input_type) == "single": 58 #if str($input_type) == "single":