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1 <?xml version="1.0" ?>
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9
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2 <tool id="qiime_feature-table_merge" name="qiime feature-table merge" version="2019.7">
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3 <description> - Combine multiple tables</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime feature-table merge
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9
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2
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10 #if $input_files_itables:
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11 #def list_dict_to_string(list_dict):
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12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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13 #for d in list_dict[1:]:
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14 #set $file_list = $file_list + ' --i-tables=' + d['additional_input'].__getattr__('file_name')
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15 #end for
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16 #return $file_list
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17 #end def
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18 --i-tables=$list_dict_to_string($input_files_itables)
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19 #end if
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20
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21
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22 #if str($poverlapmethod) != 'None':
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23 --p-overlap-method=$poverlapmethod
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24 #end if
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25
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26
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27 --o-merged-table=omergedtable
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28 ;
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29 cp omergedtable.qza $omergedtable
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30 ]]></command>
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31 <inputs>
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32 <repeat name="input_files_itables" optional="False" title="--i-tables">
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33 <param format="qza,no_unzip.zip" label="--i-tables: PATH List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" type="data"/>
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34 </repeat>
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35
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36 <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select">
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37 <option selected="True" value="None">Selection is Optional</option>
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38 <option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
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39 <option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
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40 <option value="sum">sum</option>
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41 </param>
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42 </inputs>
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43 <outputs>
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44 <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable"/>
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45 </outputs>
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46 <help><![CDATA[
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47 Combine multiple tables
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48 #######################
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49
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50 Combines feature tables using the `overlap_method` provided.
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51
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52 Parameters
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53 ----------
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54 tables : List[FeatureTable[Frequency]]
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55 The collection of feature tables to be merged.
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56 overlap_method : Str % Choices('error_on_overlapping_sample', 'error_on_overlapping_feature', 'sum'), optional
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57 Method for handling overlapping ids.
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58
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59 Returns
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60 -------
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61 merged_table : FeatureTable[Frequency]
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62 The resulting merged feature table.
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63 ]]></help>
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64 <macros>
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65 <import>qiime_citation.xml</import>
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66 </macros>
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67 <expand macro="qiime_citation"/>
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68 </tool>
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