Mercurial > repos > iuc > bbtools_bbmap

comparison bbmap.xml @ 5:6af1021d16a4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 08ae36bc77634de84d9613a71552a3e64a71a3f7"
author iuc
date Thu, 17 Mar 2022 07:42:30 +0000
parents e292ef59183d
children c7a39190a385
comparison
equal deleted inserted replaced
4:e292ef59183d 5:6af1021d16a4
1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy3" profile="@PROFILE@"> 1 <tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy4" profile="@PROFILE@">
2 <description>short-read aligner</description> 2 <description>short-read aligner</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
28 #set read2_file = 'reverse' + $ext 28 #set read2_file = 'reverse' + $ext
29 ln -s '${read2}' '${read2_file}' && 29 ln -s '${read2}' '${read2_file}' &&
30 #end if 30 #end if
31 #else: 31 #else:
32 #set read1 = $input_type_cond.reads_collection['forward'] 32 #set read1 = $input_type_cond.reads_collection['forward']
33 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name)) 33 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
34 ## bbmap uses the file extension to determine the input format. 34 ## bbmap uses the file extension to determine the input format.
35 #set ext = $read1_identifier + '.fastq' 35 #set ext = $read1_identifier + '.fastq'
36 #if $read1.ext.endswith('.gz'): 36 #if $read1.ext.endswith('.gz'):
37 #set ext = $ext + '.gz' 37 #set ext = $ext + '.gz'
38 #end if 38 #end if
39 #set read1_file = $read1_identifier + $ext 39 #set read1_file = $read1_identifier + $ext
40 ln -s '${read1}' '${read1_file}' && 40 ln -s '${read1}' '${read1_file}' &&
41 #set read2 = $input_type_cond.reads_collection['reverse'] 41 #set read2 = $input_type_cond.reads_collection['reverse']
42 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name)) 42 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
43 #set read2_file = $read2_identifier + $ext 43 #set read2_file = $read2_identifier + $ext
44 ln -s '${read2}' '${read2_file}' && 44 ln -s '${read2}' '${read2_file}' &&
45 #end if 45 #end if
46 46
47 bbmap.sh 47 bbmap.sh