view qiime2/qiime_diversity_mantel.xml @ 8:d66c7509e8f9 draft

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<?xml version="1.0" ?>
<tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.4">
	<description> - Apply the Mantel test to two distance matrices</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime diversity mantel

--i-dm1=$idm1
--i-dm2=$idm2

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

#if str($ppermutations):
 --p-permutations=$ppermutations
#end if

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



#if '__sq__' in str($plabel1):
  #set $plabel1_temp = $plabel1.replace('__sq__', "'")
  #set $plabel1 = $plabel1_temp
#end if

#if str($plabel1):
 --p-label1="$plabel1"
#end if



#if '__sq__' in str($plabel2):
  #set $plabel2_temp = $plabel2.replace('__sq__', "'")
  #set $plabel2 = $plabel2_temp
#end if

#if str($plabel2):
 --p-label2="$plabel2"
#end if



--o-visualization=ovisualization
;
qiime tools export --input-path 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]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
		<param label="--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="True" 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="True" type="text" value="Distance Matrix 2"/>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" 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/generated/skbio.stats.distance.mantel.html

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>