annotate qiime2/qiime_diversity_beta-group-significance.xml @ 16:5021f9d76de4 draft

Deleted selected files

<?xml version="1.0" ?>
<tool id="qiime_diversity_beta-group-significance" name="qiime diversity beta-group-significance"
      version="2020.8">
  <description>Beta diversity group significance</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity beta-group-significance

--i-distance-matrix=$idistancematrix
# 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($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if
#if '__cb__' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if
#if 'X' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if
#if '__sq__' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if
#if '__db__' in str($mmetadatacolumn):
  #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
  #set $mmetadatacolumn = $mmetadatacolumn_temp
#end if

--m-metadata-column=$mmetadatacolumn


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

#if $ppairwise:
 --p-pairwise
#end if

--p-permutations=$ppermutations

--o-visualization=ovisualization

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

;
cp odistancematrix.qza $odistancematrix

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

;
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-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
    <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
    </repeat>
    <param label="--m-metadata-column: COLUMN  MetadataColumn[Categorical] Categorical sample metadata column.          [required]" name="mmetadatacolumn" optional="False" type="text" />
    <param label="--p-method: " name="pmethod" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="permanova">permanova</option>
      <option value="anosim">anosim</option>
      <option value="permdisp">permdisp</option>
    </param>
    <param label="--p-pairwise: --p-pairwise: / --p-no-pairwise Perform pairwise tests between all pairs of groups in addition to the test across all groups. This can be very slow if there are a lot of groups in the metadata column.                                [default: False]" name="ppairwise" selected="False" type="boolean" />
    <param label="--p-permutations: INTEGER The number of permutations to be run when computing p-values.                                [default: 999]" name="ppermutations" optional="True" type="integer" value="999" />
    <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[
Beta diversity group significance
###############################################################

Determine whether groups of samples are significantly different from one
another using a permutation-based statistical test.

Parameters
----------
distance_matrix : DistanceMatrix
    Matrix of distances between pairs of samples.
metadata : MetadataColumn[Categorical]
    Categorical sample metadata column.
method : Str % Choices('permanova', 'anosim', 'permdisp'), optional
    The group significance test to be applied.
pairwise : Bool, optional
    Perform pairwise tests between all pairs of groups in addition to the
    test across all groups. This can be very slow if there are a lot of
    groups in the metadata column.
permutations : Int, optional
    The number of permutations to be run when computing p-values.

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