Mercurial > repos > iuc > mothur_taxonomy_to_krona

annotate taxonomy-to-krona.xml @ 0:7bfd66707e6f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 21:54:35 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool id="mothur_taxonomy_to_krona" name="Taxonomy-to-Krona" version="1.0">
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2 <description>convert a mothur taxonomy file to Krona input format</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <command detect_errors="exit_code"><![CDATA[
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7 cat $inputfile
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8 | tail -n +2 ## remove header line
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9 | cut -f2,3 ## remove first column
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10 | sed 's/;/\t/g' ## split taxonomy field on semicolon
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11 | sed 's/"//g' ## remove quotation marks
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12 | sed 's/[ \t]*$//' ## remove trailing whitespace
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13 #if $stripconfidences
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14 | sed -r 's/[(][0-9]+[)]//g' ## remove confidence scores
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15 #end if
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16 > $outputfile
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17 ]]></command>
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18 <inputs>
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19 <param name="inputfile" type="data" format="mothur.cons.taxonomy" label="Taxonomy file"
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20 help="Mothur-formatted taxonomy file. Should have 3 columns; OTU-size-taxonomy"/>
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21 <param name="stripconfidences" type="boolean" checked="false" label="Strip confidence values?"
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22 help="Strip the confidence values enclosed in parentheses behind the taxonomy levels if present. e.g. Bacteria(100);Bacteroidetes(87);.."/>
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23 </inputs>
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24 <outputs>
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25 <data name="outputfile" format="tabular" label="${tool.name} on ${on_string}: krona-formatted taxonomy file"/>
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26 </outputs>
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27 <tests>
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28 <test><!-- test defaults -->
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29 <param name="inputfile" value="example.constaxonomy"/>
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30 <output name="outputfile">
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31 <assert_contents>
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32 <has_line_matching expression="^\d+(\t[\w\d\-()]+)+$"/>
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33 <not_has_text text="Otu01"/>
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34 <not_has_text text=";"/>
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35 <has_text text="Bacteria"/>
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36 <has_text text="(100)"/>
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37 </assert_contents>
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38 </output>
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39 </test>
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40 <test><!-- test with stripping of confidence scores -->
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41 <param name="inputfile" value="example.constaxonomy"/>
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42 <param name="stripconfidences" value="true"/>
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43 <output name="outputfile">
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44 <assert_contents>
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45 <has_line_matching expression="^\d+(\t[\w\d\-]+)+$"/>
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46 <not_has_text text="Otu01"/>
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47 <not_has_text text=";"/>
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48 <has_text text="Bacteria"/>
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49 <not_has_text text="(100)"/>
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 Krona text input requires a tab-delimited file with first column being a count, and the rest representing the hierarchy, for example::
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56
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57 2 Fats Saturated fat
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58 3 Fats Unsaturated fat Monounsaturated fat
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59 3 Fats Unsaturated fat Polyunsaturated fat
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60 13 Carbohydrates Sugars
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61 4 Carbohydrates Dietary fiber
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62 21 Carbohydrates
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63 5 Protein
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64 4
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65
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66 This can be input into the Krona tool as generic text format, and would yield this `Krona plot`_.
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67
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68 .. _Krona plot: https://marbl.github.io/Krona/examples/xml.krona.html
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69
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70 ]]></help>
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71 <expand macro="citations">
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72 <citation type="doi">10.1186/1471-2105-12-385</citation>
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73 </expand>
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74 </tool>