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comparison biohansel.xml @ 9:e305df0b1af7 draft

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planemo upload for repository https://github.com/phac-nml/biohansel commit 13f8e2ed8e9de3e1437cc9632110ce5395e34191
author nml
date Mon, 22 Jul 2019 14:40:16 -0400
parents 4fa9d5e748d4
children cd6682c83b22
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8:4fa9d5e748d4 9:e305df0b1af7
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
7 <![CDATA[ 7 <![CDATA[
8 8
9 #import re 9 #import re
10 #import os
10 11
11 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38) 12 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38)
12 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$') 13 #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+)?)') 14 #set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)')
14 15
50 #return '"{}"'.format($name) if $ending in $name else '"{}{}"'.format($name, $ending) 51 #return '"{}"'.format($name) if $ending in $name else '"{}{}"'.format($name, $ending)
51 #end def 52 #end def
52 53
53 ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz) 54 ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz)
54 #if $input.type == 'fasta' 55 #if $input.type == 'fasta'
55 #set $input_files = '"{}"'.format($input.fasta.name) 56 #set $input_files = '"{}.fasta"'.format(os.path.splitext($input.fasta.name)[0])
56 ln -s "$input.fasta" $input_files && 57 ln -s "$input.fasta" $input_files &&
57 #elif $input.type == 'paired' 58 #elif $input.type == 'paired'
58 #set $forward_filename = $get_paired_fastq_filename($input.forward) 59 #set $forward_filename = $get_paired_fastq_filename($input.forward)
59 #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False) 60 #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False)
60 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename) 61 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename)