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comparison biohansel.xml @ 3:c1d05dd90ef2 draft

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planemo upload for repository https://github.com/phac-nml/biohansel commit 38c1ecfc8847bbd25f66a78bfa99c753e2cbc4d2
author nml
date Fri, 16 Nov 2018 13:10:37 -0500
parents aaab9b598c9e
children 23fbe781ce41
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2:aaab9b598c9e 3:c1d05dd90ef2
1 <tool id="biohansel" name="biohansel" version="2.1.1"> 1 <tool id="biohansel" name="biohansel" version="2.1.2">
2 <description>SNP subtyping of genome sequence reads or assemblies</description> 2 <description>SNP subtyping of genome sequence reads or assemblies</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.0">bio_hansel</requirement> 4 <requirement type="package" version="2.1.0">bio_hansel</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
8 8
9 #import re 9 #import re
10 10
11 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38) 11 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38)
12 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$') 12 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$')
13 #set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)\.fastq(\.gz|sanger)?$') 13 #set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)\.fastq(\.gz|sanger|sanger\.gz)?$')
14 14
15 #def is_gzipped_fastq($data_input) 15 #def is_gzipped_fastq($data_input)
16 ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'? 16 ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
17 #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz') 17 #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz')
18 #end def 18 #end def