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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="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime gneiss assign-ids --i-input-table=$iinputtable --i-input-tree=$iinputtree
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10
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11 #if str($cmdconfig) != 'None':
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12 --cmd-config=$cmdconfig
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13 #end if
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14 --o-output-tree=ooutputtree --o-output-table=ooutputtable;
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15
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16 cp ooutputtree.qza $ooutputtree;
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17 cp ooutputtable.qza $ooutputtable;
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param format="qza,no_unzip.zip" label="--i-input-table: FeatureTable[Frequency] The input table of counts. [required]" name="iinputtable" optional="False" type="data"/>
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22 <param format="qza,no_unzip.zip" label="--i-input-tree: Phylogeny[Rooted] The input tree with potential missing ids. [required]" name="iinputtree" optional="False" type="data"/>
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23 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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24 </inputs>
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25 <outputs>
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26 <data format="qza" label="${tool.name} on ${on_string}: output-tree.qza" name="ooutputtree"/>
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27 <data format="qza" label="${tool.name} on ${on_string}: output-table.qza" name="ooutputtable"/>
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28 </outputs>
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29 <help>
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30 <![CDATA[
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31 Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
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32 -----------------------------------------------------------------------------------------------------------
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33
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34 Assigns UUIDs to uniquely identify internal nodes in the tree. Also
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35 corrects for polytomies to create strictly bifurcating trees and aligns the
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36 table columns with the tree tip names
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37
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38 Parameters
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39 ----------
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40 input_table : FeatureTable[Frequency]
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41 The input table of counts.
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42 input_tree : Phylogeny[Rooted]
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43 The input tree with potential missing ids.
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44
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45 Returns
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46 -------
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47 output_table : FeatureTable[Frequency]
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48 A table with features matching the tree tips.
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49 output_tree : Hierarchy
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50 A tree with uniquely identifying ids.
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51 ]]>
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52 </help>
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53 </tool>
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