Mercurial > repos > iuc > bbtools_bbmap

comparison bbmap.xml @ 11:7f19559b8b55 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 20:25:42 +0000
parents 9ed6579f52f3
children 3f94a2e3d513
comparison
equal deleted inserted replaced
10:b394de3cf6e8 11:7f19559b8b55
4 <import>macros.xml</import> 4 <import>macros.xml</import>
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
10 #import re
11
12 #if str($ref_source_cond.ref_source) == 'cached' 9 #if str($ref_source_cond.ref_source) == 'cached'
13 #set ref = str($ref_source_cond.reference.fields.path) 10 #set ref = str($ref_source_cond.reference.fields.path)
14 #else: 11 #else:
15 #set ref = $ref_source_cond.reference 12 #set ref = $ref_source_cond.reference
16 #end if 13 #end if
29 #set read2_file = 'reverse' + $ext 26 #set read2_file = 'reverse' + $ext
30 ln -s '${read2}' '${read2_file}' && 27 ln -s '${read2}' '${read2_file}' &&
31 #end if 28 #end if
32 #else: 29 #else:
33 #set read1 = $input_type_cond.reads_collection['forward'] 30 #set read1 = $input_type_cond.reads_collection['forward']
34 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
35 ## bbmap uses the file extension to determine the input format. 31 ## bbmap uses the file extension to determine the input format.
36 #set ext = $read1_identifier + '.fastq' 32 #set ext = '.fastq'
37 #if $read1.ext.endswith('.gz'): 33 #if $read1.ext.endswith('.gz'):
38 #set ext = $ext + '.gz' 34 #set ext = $ext + '.gz'
39 #end if 35 #end if
40 #set read1_file = $read1_identifier + $ext 36 #set read1_file = 'forward' + $ext
41 ln -s '${read1}' '${read1_file}' && 37 ln -s '${read1}' '${read1_file}' &&
42 #set read2 = $input_type_cond.reads_collection['reverse'] 38 #set read2 = $input_type_cond.reads_collection['reverse']
43 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) 39 #set read2_file = 'reverse' + $ext
44 #set read2_file = $read2_identifier + $ext
45 ln -s '${read2}' '${read2_file}' && 40 ln -s '${read2}' '${read2_file}' &&
46 #end if 41 #end if
47 42
48 bbmap.sh 43 bbmap.sh
49 44