Mercurial > repos > greg > vsnp_determine_ref_from_data
comparison vsnp_determine_ref_from_data.xml @ 3:6116deacb2c7 draft
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author | greg |
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date | Mon, 23 Nov 2020 21:42:34 +0000 |
parents | ee6166a3edd8 |
children | 36bdf8b439ed |
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2:ee6166a3edd8 | 3:6116deacb2c7 |
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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": |