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comparison kraken.xml @ 12:33a5a81e10ee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 659d4506dad485d853a91a6a6f8bed1e3c56e204
author iuc
date Thu, 13 Sep 2018 09:43:38 -0400
parents 69e7d02d21fe
children 96f11a194da9
comparison
equal deleted inserted replaced
11:69e7d02d21fe 12:33a5a81e10ee
35 #if $single_paired.input_pair.forward.is_of_type( 'fastq' ): 35 #if $single_paired.input_pair.forward.is_of_type( 'fastq' ):
36 --fastq-input 36 --fastq-input
37 #else: 37 #else:
38 --fasta-input 38 --fasta-input
39 #end if 39 #end if
40 "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}" 40 '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}'
41 ${single_paired.check_names} 41 ${single_paired.check_names}
42 #else: 42 #else:
43 #if $single_paired.input_sequences.is_of_type('fastq') 43 #if $single_paired.input_sequences.is_of_type('fastq')
44 --fastq-input 44 --fastq-input
45 #else: 45 #else:
47 #end if 47 #end if
48 '${single_paired.input_sequences}' 48 '${single_paired.input_sequences}'
49 #end if 49 #end if
50 50
51 #if $split_reads: 51 #if $split_reads:
52 --classified-out "${classified_out}" --unclassified-out "${unclassified_out}" 52 --classified-out '${classified_out}' --unclassified-out '${unclassified_out}'
53 #end if 53 #end if
54 54
55 ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3 55 ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3
56 56
57 > "${output}" 57 > '${output}'
58 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" 58 ##kraken-translate --db '${kraken_database.fields.name}' '${output}' > '${translated}'
59 ]]></command> 59 ]]></command>
60 <inputs> 60 <inputs>
61 <conditional name="single_paired"> 61 <conditional name="single_paired">
62 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> 62 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
63 <option value="collection">Collection</option> 63 <option value="collection">Collection</option>