Mercurial > repos > iuc > mothur_taxonomy_to_krona
view taxonomy-to-krona.xml @ 3:71e7d93a593e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
author | iuc |
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date | Fri, 03 Aug 2018 14:22:22 -0400 |
parents | 7bfd66707e6f |
children | db30eb96ea23 |
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<tool id="mothur_taxonomy_to_krona" name="Taxonomy-to-Krona" version="1.0"> <description>convert a mothur taxonomy file to Krona input format</description> <macros> <import>macros.xml</import> </macros> <command detect_errors="exit_code"><![CDATA[ cat $inputfile | tail -n +2 ## remove header line | cut -f2,3 ## remove first column | sed 's/;/\t/g' ## split taxonomy field on semicolon | sed 's/"//g' ## remove quotation marks | sed 's/[ \t]*$//' ## remove trailing whitespace #if $stripconfidences | sed -r 's/[(][0-9]+[)]//g' ## remove confidence scores #end if > $outputfile ]]></command> <inputs> <param name="inputfile" type="data" format="mothur.cons.taxonomy" label="Taxonomy file" help="Mothur-formatted taxonomy file. Should have 3 columns; OTU-size-taxonomy"/> <param name="stripconfidences" type="boolean" checked="false" label="Strip confidence values?" help="Strip the confidence values enclosed in parentheses behind the taxonomy levels if present. e.g. Bacteria(100);Bacteroidetes(87);.."/> </inputs> <outputs> <data name="outputfile" format="tabular" label="${tool.name} on ${on_string}: krona-formatted taxonomy file"/> </outputs> <tests> <test><!-- test defaults --> <param name="inputfile" value="example.constaxonomy"/> <output name="outputfile"> <assert_contents> <has_line_matching expression="^\d+(\t[\w\d\-()]+)+$"/> <not_has_text text="Otu01"/> <not_has_text text=";"/> <has_text text="Bacteria"/> <has_text text="(100)"/> </assert_contents> </output> </test> <test><!-- test with stripping of confidence scores --> <param name="inputfile" value="example.constaxonomy"/> <param name="stripconfidences" value="true"/> <output name="outputfile"> <assert_contents> <has_line_matching expression="^\d+(\t[\w\d\-]+)+$"/> <not_has_text text="Otu01"/> <not_has_text text=";"/> <has_text text="Bacteria"/> <not_has_text text="(100)"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ Krona text input requires a tab-delimited file with first column being a count, and the rest representing 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 This can be input into the Krona tool as generic text format, and would yield this `Krona plot`_. .. _Krona plot: https://marbl.github.io/Krona/examples/xml.krona.html ]]></help> <expand macro="citations"> <citation type="doi">10.1186/1471-2105-12-385</citation> </expand> </tool>