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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_merge" name="qiime feature-table merge"
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3 version="2020.8">
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4 <description>Combine multiple tables</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 feature-table merge
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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($input_files_itables)
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19 # end if
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20
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21 #if str($poverlapmethod) != 'None':
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22 --p-overlap-method=$poverlapmethod
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23 #end if
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24
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25 --o-merged-table=omergedtable
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26
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27 #if str($examples) != 'None':
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28 --examples=$examples
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29 #end if
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30
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31 ;
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32 cp omergedtable.qza $omergedtable
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33
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34 ]]></command>
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35 <inputs>
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36 <repeat name="input_files_itables" optional="False" title="--i-tables">
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37 <param format="qza,no_unzip.zip" label="--i-tables: ARTIFACTS... List[FeatureTable[Frequency]] The collection of feature tables to be merged. [required]" name="additional_input" optional="False" type="data" />
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38 </repeat>
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39 <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select">
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40 <option selected="True" value="None">Selection is Optional</option>
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41 <option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
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42 <option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
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43 <option value="sum">sum</option>
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44 </param>
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45 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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46
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47 </inputs>
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48
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49 <outputs>
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50 <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable" />
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51
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52 </outputs>
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53
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54 <help><![CDATA[
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55 Combine multiple tables
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56 ###############################################################
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57
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58 Combines feature tables using the `overlap_method` provided.
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59
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60 Parameters
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61 ----------
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62 tables : List[FeatureTable[Frequency]]
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63 The collection of feature tables to be merged.
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64 overlap_method : Str % Choices('error_on_overlapping_sample', 'error_on_overlapping_feature', 'sum'), optional
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65 Method for handling overlapping ids.
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66
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67 Returns
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68 -------
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69 merged_table : FeatureTable[Frequency]
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70 The resulting merged feature table.
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71 ]]></help>
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72 <macros>
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73 <import>qiime_citation.xml</import>
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74 </macros>
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75 <expand macro="qiime_citation"/>
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76 </tool> |
