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1 <?xml version="1.0" ?>
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2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse"
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3 version="2020.8">
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4 <description>Collapse features by their taxonomy at the specified level</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 taxa collapse
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10
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11 --i-table=$itable
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12
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13 --i-taxonomy=$itaxonomy
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14
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15 --p-level=$plevel
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16
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17 --o-collapsed-table=ocollapsedtable
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18
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19 #if str($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 ocollapsedtable.qza $ocollapsedtable
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25
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26 ]]></command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data" />
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29 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data" />
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30 <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" type="text" />
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31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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32
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33 </inputs>
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34
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35 <outputs>
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36 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable" />
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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 Collapse features by their taxonomy at the specified level
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42 ###############################################################
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43
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44 Collapse groups of features that have the same taxonomic assignment through
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45 the specified level. The frequencies of all features will be summed when
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46 they are collapsed.
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47
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48 Parameters
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49 ----------
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50 table : FeatureTable[Frequency]
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51 Feature table to be collapsed.
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52 taxonomy : FeatureData[Taxonomy]
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53 Taxonomic annotations for features in the provided feature table. All
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54 features in the feature table must have a corresponding taxonomic
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55 annotation. Taxonomic annotations that are not present in the feature
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56 table will be ignored.
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57 level : Int
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58 The taxonomic level at which the features should be collapsed. All
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59 ouput features will have exactly this many levels of taxonomic
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60 annotation.
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61
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62 Returns
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63 -------
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64 collapsed_table : FeatureTable[Frequency]
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65 The resulting feature table, where all features are now taxonomic
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66 annotations with the user-specified number of levels.
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67 ]]></help>
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68 <macros>
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69 <import>qiime_citation.xml</import>
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70 </macros>
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71 <expand macro="qiime_citation"/>
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72 </tool> |
