<?xml version="1.0" ?>
<tool id="qiime_diversity_mantel" name="qiime diversity mantel"
      version="2020.8">
  <description>Apply the Mantel test to two distance matrices</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity mantel

--i-dm1=$idm1

--i-dm2=$idm2

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

--p-permutations=$ppermutations

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

#if str($plabel1):
  --p-label1=$plabel1
#end if
#if str($plabel2):
  --p-label2=$plabel2
#end if
--o-visualization=ovisualization

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

;
cp ofiltereddistancematrix.qza $ofiltereddistancematrix

;
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-dm1: ARTIFACT     Matrix of distances between pairs of samples. DistanceMatrix                                                  [required]" name="idm1" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT     Matrix of distances between pairs of samples. DistanceMatrix                                                  [required]" name="idm2" optional="False" type="data" />
    <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-permutations: INTEGER Range(0, None)     The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired).               [default: 999]" min="0" name="ppermutations" optional="True" type="integer" value="999" />
    <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs.                                   [default: False]" name="pintersectids" selected="False" type="boolean" />
    <param label="--p-label1: TEXT      Label for `dm1` in the output visualization. [default: \'Distance Matrix 1\']" name="plabel1" optional="False" type="text" value="\'Distance Matrix 1\'" />
    <param label="--p-label2: TEXT      Label for `dm2` in the output visualization. [default: \'Distance Matrix 2\']" name="plabel2" optional="False" type="text" value="\'Distance Matrix 2\'" />
    <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[
Apply the Mantel test to two distance matrices
###############################################################

Apply a two-sided Mantel test to identify correlation between two distance
matrices.  Note: the directionality of the comparison has no bearing on the
results. Thus, comparing distance matrix X to distance matrix Y is
equivalent to comparing Y to X.  Note: the order of samples within the two
distance matrices does not need to be the same; the distance matrices will
be reordered before applying the Mantel test.  See the scikit-bio docs for
more details about the Mantel test:  http://scikit-
bio.org/docs/latest/generated/skbio.stats.distance.mantel

Parameters
----------
dm1 : DistanceMatrix
    Matrix of distances between pairs of samples.
dm2 : DistanceMatrix
    Matrix of distances between pairs of samples.
method : Str % Choices('spearman', 'pearson'), optional
    The correlation test to be applied in the Mantel test.
permutations : Int % Range(0, None), optional
    The number of permutations to be run when computing p-values. Supplying
    a value of zero will disable permutation testing and p-values will not
    be calculated (this results in *much* quicker execution time if
    p-values are not desired).
intersect_ids : Bool, optional
    If supplied, IDs that are not found in both distance matrices will be
    discarded before applying the Mantel test. Default behavior is to error
    on any mismatched IDs.
label1 : Str, optional
    Label for `dm1` in the output visualization.
label2 : Str, optional
    Label for `dm2` in the output visualization.

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