Mercurial > repos > iuc > bbtools_bbduk

comparison bbduk.xml @ 7:bf0cb5dd02f2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
author iuc
date Wed, 24 Apr 2024 20:24:48 +0000
parents 425dab0e057b
children d1f62024a08b
comparison
equal deleted inserted replaced
6:1c427e24fb79 7:bf0cb5dd02f2
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #import os 9 #import os
10 #import re
11 10
12 #if str($input_type_cond.input_type) in ['single', 'pair']: 11 #if str($input_type_cond.input_type) in ['single', 'pair']:
13 #set read1 = $input_type_cond.read1 12 #set read1 = $input_type_cond.read1
14 ## bbduk uses the file extension to determine the input format. 13 ## bbduk uses the file extension to determine the input format.
15 #set ext = '.fastq' 14 #set ext = '.fastq'
23 #set read2_file = 'reverse' + $ext 22 #set read2_file = 'reverse' + $ext
24 ln -s '${read2}' '${read2_file}' && 23 ln -s '${read2}' '${read2_file}' &&
25 #end if 24 #end if
26 #else: 25 #else:
27 #set read1 = $input_type_cond.reads_collection['forward'] 26 #set read1 = $input_type_cond.reads_collection['forward']
28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
29 ## bbduk uses the file extension to determine the input format. 27 ## bbduk uses the file extension to determine the input format.
30 #set ext = $read1_identifier + '.fastq' 28 #set ext = '.fastq'
31 #if $read1.ext.endswith('.gz'): 29 #if $read1.ext.endswith('.gz'):
32 #set ext = $ext + '.gz' 30 #set ext = $ext + '.gz'
33 #end if 31 #end if
34 #set read1_file = $read1_identifier + $ext 32 #set read1_file = 'forward' + $ext
35 ln -s '${read1}' '${read1_file}' && 33 ln -s '${read1}' '${read1_file}' &&
36 #set read2 = $input_type_cond.reads_collection['reverse'] 34 #set read2 = $input_type_cond.reads_collection['reverse']
37 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name)) 35 #set read2_file = 'reverse' + $ext
38 #set read2_file = $read2_identifier + $ext
39 ln -s '${read2}' '${read2_file}' && 36 ln -s '${read2}' '${read2_file}' &&
40 #end if 37 #end if
41 38
42 #if str($reference_type_cond.reference_type) == 'files': 39 #if str($reference_type_cond.reference_type) == 'files':
43 #set refs = list() 40 #set refs = list()