comparison biohansel.xml @ 6:ba6a0af656a6 draft

planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af

5:c0b8de7aa02e

<tool id="biohansel" name="biohansel" version="2.1.4">
  <description>SNP subtyping of genome sequence reads or assemblies</description>
  <requirements>
    <requirement type="package" version="2.1.1">bio_hansel</requirement>
  </requirements>
  <command detect_errors="exit_code">

#import re

## 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 = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)\.fastq(\.gz|sanger|sanger\.gz)?$')

#def is_gzipped_fastq($data_input)
  ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
  #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz')
#end def

  #set $illumina_match = $ILLUMINA_REGEX.match($name)
  #set $fastq_dump_match = $FASTQ_DUMP_REGEX.match($name)

  #if $illumina_match
    #return $illumina_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
#end def

6:ba6a0af656a6

<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>
  </requirements>
  <command detect_errors="exit_code">

#import re

## 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+)?)')

#def is_gzipped_fastq($data_input)
  ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'?
  #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz')
#end def

  #set $illumina_match = $ILLUMINA_REGEX.match($name)
  #set $fastq_dump_match = $FASTQ_DUMP_REGEX.match($name)

  #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)
  #else    
    #return $name
  #end if
#end def