view qiime2-2020.8/qiime_feature-table_merge.xml @ 22:292c84bd5ab6 draft

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<?xml version="1.0" ?>
<tool id="qiime_feature-table_merge" name="qiime feature-table merge"
      version="2020.8">
  <description>Combine multiple tables</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime feature-table merge
# if $input_files_itables:
  # def list_dict_to_string(list_dict):
    # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
    # for d in list_dict[1:]:
      # set $file_list = $file_list + ' --i-tables=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--i-tables=$list_dict_to_string($input_files_itables)
# end if

#if str($poverlapmethod) != 'None':
--p-overlap-method=$poverlapmethod
#end if

--o-merged-table=omergedtable

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp omergedtable.qza $omergedtable

  ]]></command>
  <inputs>
    <repeat name="input_files_itables" optional="False" title="--i-tables">
      <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" />
    </repeat>
    <param label="--p-overlap-method: " name="poverlapmethod" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="error_on_overlapping_sample">error_on_overlapping_sample</option>
      <option value="error_on_overlapping_feature">error_on_overlapping_feature</option>
      <option value="sum">sum</option>
    </param>
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="qza" label="${tool.name} on ${on_string}: mergedtable.qza" name="omergedtable" />
    
  </outputs>

  <help><![CDATA[
Combine multiple tables
###############################################################

Combines feature tables using the `overlap_method` provided.

Parameters
----------
tables : List[FeatureTable[Frequency]]
    The collection of feature tables to be merged.
overlap_method : Str % Choices('error_on_overlapping_sample', 'error_on_overlapping_feature', 'sum'), optional
    Method for handling overlapping ids.

Returns
-------
merged_table : FeatureTable[Frequency]
    The resulting merged feature table.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>