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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.4">
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3 <description> - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</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 gneiss assign-ids
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9
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10 --i-input-table=$iinputtable
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11 --i-input-tree=$iinputtree
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12
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13 --o-output-table=ooutputtable
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14 --o-output-tree=ooutputtree
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15 ;
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16 cp ooutputtable.qza $ooutputtable;
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17 cp ooutputtree.qza $ooutputtree
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18 ]]></command>
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19 <inputs>
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20 <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data"/>
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21 <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data"/>
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22 </inputs>
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23 <outputs>
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24 <data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable"/>
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25 <data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree"/>
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26 </outputs>
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27 <help><![CDATA[
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28 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
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29 ##########################################################################################################
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30
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31 Assigns UUIDs to uniquely identify internal nodes in the tree. Also
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32 corrects for polytomies to create strictly bifurcating trees and aligns the
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33 table columns with the tree tip names
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34
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35 Parameters
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36 ----------
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37 input_table : FeatureTable[Frequency]
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38 The input table of counts.
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39 input_tree : Phylogeny[Rooted]
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40 The input tree with potential missing ids.
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41
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42 Returns
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43 -------
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44 output_table : FeatureTable[Frequency]
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45 A table with features matching the tree tips.
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46 output_tree : Hierarchy
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47 A tree with uniquely identifying ids.
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48 ]]></help>
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49 <macros>
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50 <import>qiime_citation.xml</import>
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51 </macros>
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52 <expand macro="qiime_citation"/>
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53 </tool>
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