view qiime2-2020.8/qiime_longitudinal_nmit.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_longitudinal_nmit" name="qiime longitudinal nmit"
      version="2020.8">
  <description>Nonparametric microbial interdependence test</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime longitudinal nmit

--i-table=$itable
# if $input_files_mmetadatafile:
  # 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 + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
# end if

#if '__ob__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__cb__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if 'X' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__sq__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__db__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if

--p-individual-id-column=$pindividualidcolumn


#if str($pcorrmethod) != 'None':
--p-corr-method=$pcorrmethod
#end if

#if str($pdistmethod) != 'None':
--p-dist-method=$pdistmethod
#end if

--o-distance-matrix=odistancematrix

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

;
cp odistancematrix.qza $odistancematrix

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table to use for microbial interdependence test.                                       [required]" name="itable" optional="False" type="data" />
    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple           Sample metadata file containing individual-id-column. arguments will be merged)                                                        [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                   [required]" name="pindividualidcolumn" optional="False" type="text" />
    <param label="--p-corr-method: " name="pcorrmethod" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="kendall">kendall</option>
      <option value="pearson">pearson</option>
      <option value="spearman">spearman</option>
    </param>
    <param label="--p-dist-method: " name="pdistmethod" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="fro">fro</option>
      <option value="nuc">nuc</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}: distancematrix.qza" name="odistancematrix" />
    
  </outputs>

  <help><![CDATA[
Nonparametric microbial interdependence test
###############################################################

Perform nonparametric microbial interdependence test to determine
longitudinal sample similarity as a function of temporal microbial
composition. For more details and citation, please see
doi.org/10.1002/gepi.22065

Parameters
----------
table : FeatureTable[RelativeFrequency]
    Feature table to use for microbial interdependence test.
metadata : Metadata
    Sample metadata file containing individual_id_column.
individual_id_column : Str
    Metadata column containing IDs for individual subjects.
corr_method : Str % Choices('kendall', 'pearson', 'spearman'), optional
    The temporal correlation test to be applied.
dist_method : Str % Choices('fro', 'nuc'), optional
    Temporal distance method, see numpy.linalg.norm for details.

Returns
-------
distance_matrix : DistanceMatrix
    The resulting distance matrix.
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>