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1 <?xml version="1.0" ?>
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2 <tool id="qiime_taxa_collapse" name="qiime taxa collapse" version="2019.4">
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3 <description> - Collapse features by their taxonomy at the specified level</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime taxa collapse
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9
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10 --i-table=$itable
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11 --i-taxonomy=$itaxonomy
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12 --p-level="$plevel"
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13
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14 --o-collapsed-table=ocollapsedtable
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15 ;
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16 cp ocollapsedtable.qza $ocollapsedtable
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17 ]]></command>
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18 <inputs>
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19 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed. [required]" name="itable" optional="False" type="data"/>
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20 <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored. [required]" name="itaxonomy" optional="False" type="data"/>
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21 <param label="--p-level: INTEGER The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation. [required]" name="plevel" optional="False" value="" type="integer"/>
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22 </inputs>
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23 <outputs>
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24 <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable"/>
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25 </outputs>
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26 <help><![CDATA[
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27 Collapse features by their taxonomy at the specified level
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28 ##########################################################
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29
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30 Collapse groups of features that have the same taxonomic assignment through
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31 the specified level. The frequencies of all features will be summed when
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32 they are collapsed.
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33
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34 Parameters
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35 ----------
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36 table : FeatureTable[Frequency]
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37 Feature table to be collapsed.
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38 taxonomy : FeatureData[Taxonomy]
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39 Taxonomic annotations for features in the provided feature table. All
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40 features in the feature table must have a corresponding taxonomic
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41 annotation. Taxonomic annotations that are not present in the feature
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42 table will be ignored.
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43 level : Int
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44 The taxonomic level at which the features should be collapsed. All
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45 ouput features will have exactly this many levels of taxonomic
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46 annotation.
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47
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48 Returns
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49 -------
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50 collapsed_table : FeatureTable[Frequency]
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51 The resulting feature table, where all features are now taxonomic
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52 annotations with the user-specified number of levels.
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53 ]]></help>
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54 <macros>
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55 <import>qiime_citation.xml</import>
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56 </macros>
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57 <expand macro="qiime_citation"/>
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58 </tool>
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