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comparison vsnp_statistics.xml @ 16:44b07199be73 draft

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author greg
date Tue, 03 Aug 2021 19:39:55 +0000
parents ce1f889b3340
children 076069733de7
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15:e5d08707e81f 16:44b07199be73
1 <tool id="vsnp_statistics" name="vSNP: statistics" version="@WRAPPER_VERSION@.1+galaxy0" profile="@PROFILE@"> 1 <tool id="vsnp_statistics" name="vSNP: statistics" version="@WRAPPER_VERSION@.2+galaxy0" profile="@PROFILE@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
19 ln -s '${read1}' '${read1_identifier}' && 19 ln -s '${read1}' '${read1_identifier}' &&
20 #if $input_type_cond.input_type == "pair": 20 #if $input_type_cond.input_type == "pair":
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 #else:
25 #set read2 = None
26 #end if 24 #end if
27 #else: 25 #else:
28 #set read1 = $input_type_cond.reads_collection['forward'] 26 #set read1 = $input_type_cond.reads_collection.forward
29 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) 27 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
30 ln -s '${read1}' '${read1_identifier}' && 28 ln -s '${read1}' '${read1_identifier}' &&
31 #set read2 = $input_type_cond.reads_collection['reverse'] 29 #set read2 = $input_type_cond.reads_collection.reverse
32 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 30 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
33 ln -s '${read2}' '${read2_identifier}' && 31 ln -s '${read2}' '${read2_identifier}' &&
34 #end if 32 #end if
35 33
36 python '$__tool_directory__/vsnp_statistics.py' 34 python '$__tool_directory__/vsnp_statistics.py'
37 --read1 '${read1_identifier}' 35 --read1 '${read1_identifier}'
38 #if $read2 is not None 36 #if $input_type_cond.input_type in ["pair", "paired"]:
39 --read2 '${read2_identifier}' 37 --read2 '${read2_identifier}'
40 #end if 38 #end if
41 #if $read1.is_of_type('fastqsanger.gz'): 39 #if $read1.is_of_type('fastqsanger.gz'):
42 --gzipped 40 --gzipped
43 #end if 41 #end if