Mercurial > repos > petr-novak > krona_text
changeset 0:04021cfd5170 draft default tip
planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 5269b4297ea690bce0802c3c1cb217f24290f1ec-dirty
author | petr-novak |
---|---|
date | Mon, 04 Mar 2024 09:16:34 +0000 |
parents | |
children | |
files | README krona_text.xml |
diffstat | 2 files changed, 72 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Mar 04 09:16:34 2024 +0000 @@ -0,0 +1,14 @@ +Krona visualistion on generic hierarchy files. + +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 \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/krona_text.xml Mon Mar 04 09:16:34 2024 +0000 @@ -0,0 +1,58 @@ +<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>