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1 <?xml version="1.0" ?>
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2 <tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental"
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3 version="2020.8">
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4 <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime fragment-insertion classify-otus-experimental
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10
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11 --i-representative-sequences=$irepresentativesequences
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12
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13 --i-tree=$itree
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14
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15 --i-reference-taxonomy=$ireferencetaxonomy
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16
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17 --o-classification=oclassification
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18
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19 #if str($examples) != 'None':
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20 --examples=$examples
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21 #end if
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22
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23 ;
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24 cp oclassification.qza $oclassification
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25
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26 ]]></command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a \'sepp\' run to produce the \'tree\'. [required]" name="irepresentativesequences" optional="False" type="data" />
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29 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function \'sepp\' [required]" name="itree" optional="False" type="data" />
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30 <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string. [required]" name="ireferencetaxonomy" optional="False" type="data" />
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31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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32
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33 </inputs>
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34
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35 <outputs>
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36 <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
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37
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38 </outputs>
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39
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40 <help><![CDATA[
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41 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
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42 ###############################################################
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43
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44
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45 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
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46 for every inserted fragment. Then, look up the reference lineage string in
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47 the reference taxonomy.
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48
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49 Parameters
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50 ----------
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51 representative_sequences : FeatureData[Sequence]
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52 The sequences used for a 'sepp' run to produce the 'tree'.
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53 tree : Phylogeny[Rooted]
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54 The tree resulting from inserting fragments into a reference phylogeny,
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55 i.e. the output of function 'sepp'
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56 reference_taxonomy : FeatureData[Taxonomy]
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57 Reference taxonomic table that maps every OTU-ID into a taxonomic
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58 lineage string.
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59
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60 Returns
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61 -------
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62 classification : FeatureData[Taxonomy]
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63 Taxonomic lineages for inserted fragments.
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64 ]]></help>
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65 <macros>
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66 <import>qiime_citation.xml</import>
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67 </macros>
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68 <expand macro="qiime_citation"/>
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69 </tool> |
