Mercurial > repos > nml > biohansel
changeset 6:ba6a0af656a6 draft
planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
| author | nml |
|---|---|
| date | Wed, 20 Mar 2019 13:44:02 -0400 |
| parents | c0b8de7aa02e |
| children | 3360158bb0c5 |
| files | biohansel.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/biohansel.xml Mon Mar 11 14:27:21 2019 -0400 +++ b/biohansel.xml Wed Mar 20 13:44:02 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="biohansel" name="biohansel" version="2.1.4"> +<tool id="biohansel" name="biohansel" version="2.1.5"> <description>SNP subtyping of genome sequence reads or assemblies</description> <requirements> <requirement type="package" version="2.1.1">bio_hansel</requirement> @@ -10,7 +10,7 @@ ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38) #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$') -#set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)\.fastq(\.gz|sanger|sanger\.gz)?$') +#set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)') #def is_gzipped_fastq($data_input) ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'? @@ -29,12 +29,12 @@ #if $illumina_match #return $illumina_match.group(1) + #elif $fastq_dump_match + #return $fastq_dump_match.group(1) #elif $re.search(r'_R(1|2)', $name): #return $re.sub(r'(.+)_R(1|2)([^\.]*)(\..+)', r'\1\3', $name) #elif $re.match(r'.+_\d\.', $name): #return $re.sub(r'(.+)_(\d)(\..+)', r'\1', $name) - #elif $fastq_dump_match - #return $fastq_dump_match.group(1) #else #return $name #end if