Mercurial > repos > nml > biohansel
comparison biohansel.xml @ 3:c1d05dd90ef2 draft
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 |
comparison
equal
deleted
inserted
replaced
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 |