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view krona_text.xml @ 0:04021cfd5170 draft default tip
planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 5269b4297ea690bce0802c3c1cb217f24290f1ec-dirty
author | petr-novak |
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date | Mon, 04 Mar 2024 09:16:34 +0000 |
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<tool id="krona-text" name="Visualize with Krona" version="1.1"> <description>Visualise any hierarchical data</description> <requirements> <requirement type="package" version="2.6">krona</requirement> </requirements> <command><![CDATA[ echo "starting" && head '${inputfile}' && #if "$isMothur" == "Y" awk 'BEGIN{FS="\t";OFS="\t"}{print $2,$3}' '${inputfile}' > tempinput && head tempinput && sed -i 's/;/\t/g' tempinput && #else cp '${inputfile}' tempinput && #end if head tempinput && export TERM=dumb && ktImportText tempinput ]]></command> <inputs> <!-- parameter examples, see https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax for descriptions --> <!-- file from history --> <param name="inputfile" type="data" label="Select input file" help="Choose input file from history. Format: count - Hierarchy (tab separated)"/> <param name="isMothur" type="boolean" checked="False" truevalue="Y" falsevalue="N" label="is this output from MOTHUR?" help="e.g. taxonomy file generated from Classify.otu?"/> </inputs> <outputs> <data format="html" name="outputfile" from_work_dir="text.krona.html" label="Krona on ${on_string}: HTML"/> </outputs> <help> Input file must be a tab-delimited file with first column being a count, rest the hierarchy, for example:: 2 Fats Saturated fat 3 Fats Unsaturated fat Monounsaturated fat 3 Fats Unsaturated fat Polyunsaturated fat 13 Carbohydrates Sugars 4 Carbohydrates Dietary fiber 21 Carbohydrates 5 Protein 4 Would yield the following graph: http://krona.sourceforge.net/examples/text.krona.html This tool is a modification of https://toolshed.g2.bx.psu.edu/view/saskia-hiltemann/krona_text/b14f1444e464 </help> </tool>