Mercurial > repos > thanhlv > krona
changeset 0:4fd819e640cf draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krona commit e7f80ce946a5c29bc821e6bde51e8ab681109194-dirty
| author | thanhlv |
|---|---|
| date | Wed, 18 Sep 2019 08:26:00 -0400 |
| parents | |
| children | e4af33a5d672 |
| files | krona.xml |
| diffstat | 1 files changed, 33 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/krona.xml Wed Sep 18 08:26:00 2019 -0400 @@ -0,0 +1,33 @@ +<tool id="krona_qib" name="krona" version="2.7.1"> + <description> Interactively explore metagenomes and more from a web browser</description> + <version_command>ktImportKrona | grep -o "[0-9]\.[0-9]\.[0-9]"</version_command> + <command detect_errors="exit_code"><![CDATA[ + #if str($mode) == 'kraken2' + cat '$classified' | cut -f 2,3 > tmp_file + #else if str($mode) == 'centrifuge' + cat '$classified' | cut -f 1,3 > tmp_file + #end if + ktImportTaxonomy tmp_file + ]]> </command> + + <inputs> + <param name="mode" type="select" label="Classifier"> + <option value="kraken2">Kraken2</option> + <option value="centrifuge">Centrifuge</option> + </param> + <param name="classified" type="data" format="text,tabular" label="Select a classification file" help="Classification file from Kraken2 or Centrifuge"/> + </inputs> + + <outputs> + <data name="output_file" format="html" label="${tool.name} on ${on_string}: Krona Visualisation" from_work_dir="taxonomy.krona.html"/> + </outputs> + + <!-- <tests> + </tests> --> + + <help><![CDATA[ + ]]> </help> + <citations> + <citation type="doi">10.1186/1471-2105-12-385</citation> + </citations> +</tool>