Mercurial > repos > iuc > bbtools_bbmap
comparison bbmap.xml @ 11:7f19559b8b55 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
author | iuc |
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date | Wed, 24 Apr 2024 20:25:42 +0000 |
parents | 9ed6579f52f3 |
children | 3f94a2e3d513 |
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10:b394de3cf6e8 | 11:7f19559b8b55 |
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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 |