Mercurial > repos > devteam > kraken
comparison kraken.xml @ 7:658d47fd33e3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 659d4506dad485d853a91a6a6f8bed1e3c56e204
author | iuc |
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date | Thu, 13 Sep 2018 09:44:31 -0400 |
parents | 2fdac3e78553 |
children | 8ba2174315aa |
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6:2fdac3e78553 | 7:658d47fd33e3 |
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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> |