annotate qiime2/qiime_diversity_alpha-correlation.xml @ 16:5021f9d76de4 draft

Deleted selected files

<?xml version="1.0" ?>
<tool id="qiime_diversity_alpha-correlation" name="qiime diversity alpha-correlation"
      version="2020.8">
  <description>Alpha diversity correlation</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity alpha-correlation

--i-alpha-diversity=$ialphadiversity
# 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 str($pmethod) != 'None':
--p-method=$pmethod
#end if

#if $pintersectids:
 --p-intersect-ids
#end if

--o-visualization=ovisualization

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

;
cp oalphadiversity.qza $oalphadiversity

;
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-alpha-diversity: ARTIFACT SampleData[AlphaDiversity] Vector of alpha diversity values by sample.  [required]" name="ialphadiversity" 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          The sample metadata. arguments will be merged)                                                     [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param label="--p-method: " name="pmethod" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="spearman">spearman</option>
      <option value="pearson">pearson</option>
    </param>
    <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both the alpha diversity vector and metadata will be discarded before calculating the correlation. Default behavior is to error on any mismatched IDs.           [default: False]" name="pintersectids" selected="False" type="boolean" />
    <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[
Alpha diversity correlation
###############################################################

Determine whether numeric sample metadata columns are correlated with alpha
diversity.

Parameters
----------
alpha_diversity : SampleData[AlphaDiversity]
    Vector of alpha diversity values by sample.
metadata : Metadata
    The sample metadata.
method : Str % Choices('spearman', 'pearson'), optional
    The correlation test to be applied.
intersect_ids : Bool, optional
    If supplied, IDs that are not found in both the alpha diversity vector
    and metadata will be discarded before calculating the correlation.
    Default behavior is to error on any mismatched IDs.

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