diff qiime2-2020.8/qiime_diversity_mantel.xml @ 20:d93d8888f0b0 draft

Uploaded

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+++ b/qiime2-2020.8/qiime_diversity_mantel.xml	Fri Sep 04 12:44:24 2020 +0000
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+<?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>
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