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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 659d4506dad485d853a91a6a6f8bed1e3c56e204 |
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modified:
kraken.xml macros.xml |
| b |
| diff -r 2fdac3e78553 -r 658d47fd33e3 kraken.xml --- a/kraken.xml Mon Aug 07 17:29:06 2017 -0400 +++ b/kraken.xml Thu Sep 13 09:44:31 2018 -0400 |
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| @@ -37,7 +37,7 @@ #else: --fasta-input #end if - "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}" + '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}' ${single_paired.check_names} #else: #if $single_paired.input_sequences.is_of_type('fastq') @@ -49,13 +49,13 @@ #end if #if $split_reads: - --classified-out "${classified_out}" --unclassified-out "${unclassified_out}" + --classified-out '${classified_out}' --unclassified-out '${unclassified_out}' #end if ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3 - > "${output}" - ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" + > '${output}' + ##kraken-translate --db '${kraken_database.fields.name}' '${output}' > '${translated}' ]]></command> <inputs> <conditional name="single_paired"> |
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| diff -r 2fdac3e78553 -r 658d47fd33e3 macros.xml --- a/macros.xml Mon Aug 07 17:29:06 2017 -0400 +++ b/macros.xml Thu Sep 13 09:44:31 2018 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">1.2.3</token> + <token name="@WRAPPER_VERSION@">1.2.4</token> <xml name="requirements"> <requirements> <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement> @@ -23,6 +23,6 @@ <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations> </xml> - <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token> - <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token> + <token name="@INPUT_DATABASE@">--db '${kraken_database.fields.name}'</token> + <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH='${kraken_database.fields.path}'</token> </macros> |