Mercurial > repos > devteam > kraken
diff 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 |
---|---|
date | Thu, 13 Sep 2018 09:44:31 -0400 |
parents | 2fdac3e78553 |
children | 8ba2174315aa |
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--- a/kraken.xml Mon Aug 07 17:29:06 2017 -0400 +++ b/kraken.xml Thu Sep 13 09:44:31 2018 -0400 @@ -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">