annotate qiime2-2020.8/qiime_emperor_biplot.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_emperor_biplot" name="qiime emperor biplot"
      version="2020.8">
  <description>Visualize and Interact with Principal Coordinates Analysis Biplot</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime emperor biplot

--i-biplot=$ibiplot
# if $input_files_msamplemetadatafile:
  # 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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
# end if
# if $input_files_mfeaturemetadatafile:
  # 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-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
    # end for
    # return $file_list
  # end def
--m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
# end if

#if $pignoremissingsamples:
 --p-ignore-missing-samples
#end if

#if $pinvert:
 --p-invert
#end if

--p-number-of-features=$pnumberoffeatures

--o-visualization=ovisualization

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

;
cp odistancematrix.qza $odistancematrix

;
qiime tools export  ovisualization.qzv --output-path out
&& mkdir -p '$ovisualization.files_path'
&& cp -r out/* '$ovisualization.files_path'
&& mv '$ovisualization.files_path/index.html' '$ovisualization'

  ]]></command>
  <inputs>
    <param format="qza,no_unzip.zip" label="--i-biplot: ARTIFACT PCoAResults % Properties(\'biplot\') The principal coordinates matrix to be plotted. [required]" name="ibiplot" optional="False" type="data" />
    <repeat name="input_files_msamplemetadatafile" optional="False" title="--m-sample-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple          The sample metadata arguments will be merged)                                                     [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA... (multiple          The feature metadata (useful to manipulate the arrows arguments will    in the plot). be merged)                                                     [optional]" name="additional_input" optional="True" type="data" />
    </repeat>
    <param label="--p-ignore-missing-samples: --p-ignore-missing-samples: / --p-no-ignore-missing-samples This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: \'This sample has no metadata\'. This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata.               [default: False]" name="pignoremissingsamples" selected="False" type="boolean" />
    <param label="--p-invert: --p-invert: / --p-no-invert If specified, the point and arrow coordinates will be swapped.                               [default: False]" name="pinvert" selected="False" type="boolean" />
    <param label="--p-number-of-features: INTEGER Range(1, None)     The number of most important features (arrows) to display in the ordination. “Importance” is calculated for each feature based on the vector’s magnitude (euclidean distance from origin).          [default: 5]" min="1" name="pnumberoffeatures" optional="True" type="integer" value="5" />
    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
    
  </inputs>

  <outputs>
    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
    
  </outputs>

  <help><![CDATA[
Visualize and Interact with Principal Coordinates Analysis Biplot
###############################################################

Generates an interactive ordination biplot where the user can visually
integrate sample and feature metadata. Vectors representing the n most
important features are then plotted in the emperor visualization (5
largest, by default).

Parameters
----------
biplot : PCoAResults % Properties('biplot')
    The principal coordinates matrix to be plotted.
sample_metadata : Metadata
    The sample metadata
feature_metadata : Metadata, optional
    The feature metadata (useful to manipulate the arrows in the plot).
ignore_missing_samples : Bool, optional
    This will suppress the error raised when the coordinates matrix
    contains samples that are not present in the metadata. Samples without
    metadata are included by setting all metadata values to: "This sample
    has no metadata". This flag is only applied if at least one sample is
    present in both the coordinates matrix and the metadata.
invert : Bool, optional
    If specified, the point and arrow coordinates will be swapped.
number_of_features : Int % Range(1, None), optional
    The number of most important features (arrows) to display in the
    ordination. “Importance” is calculated for each feature based on the
    vector’s magnitude (euclidean distance from origin).

Returns
-------
visualization : Visualization
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>