diff qiime2/qiime_diversity_adonis.xml @ 29:3ba9833030c1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity_adonis.xml	Fri Sep 04 13:12:49 2020 +0000
@@ -0,0 +1,108 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity_adonis" name="qiime diversity adonis"
+      version="2020.8">
+  <description>adonis PERMANOVA test for beta group significance</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime diversity adonis
+
+--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($input_files_mmetadatafile)
+# end if
+
+--p-formula=$pformula
+
+--p-permutations=$ppermutations
+
+--p-n-jobs=$pnjobs
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp osubsampledsequences.qza $osubsampledsequences
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-distance-matrix: ARTIFACT DistanceMatrix     Matrix of distances between pairs of samples. [required]" name="idistancematrix" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple          Sample metadata containing formula terms. arguments will be merged)                                                     [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-formula: TEXT     Model formula containing only independent terms contained in the sample metadata. These can be continuous variables or factors, and they can have interactions as in a typical R formula. E.g., the formula \'treatment+block\' would test whether the input distance matrix partitions based on \'treatment\' and \'block\' sample metadata. The formula \'treatment*block\' would test both of those effects as well as their interaction. Enclose formulae in quotes to avoid unpleasant surprises.                        [required]" name="pformula" optional="False" type="text" />
+    <param label="--p-permutations: INTEGER Range(1, None)     The number of permutations to be run when computing p-values.                                [default: 999]" min="1" name="ppermutations" optional="True" type="integer" value="999" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
+adonis PERMANOVA test for beta group significance
+###############################################################
+
+Determine whether groups of samples are significantly different from one
+another using the ADONIS permutation-based statistical test in vegan-R. The
+function partitions sums of squares of a multivariate data set, and is
+directly analogous to MANOVA (multivariate analysis of variance). This
+action differs from beta_group_significance in that it accepts R formulae
+to perform multi-way ADONIS tests; beta_group_signficance only performs
+one-way tests. For more details see
+http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/adonis.html
+
+Parameters
+----------
+distance_matrix : DistanceMatrix
+    Matrix of distances between pairs of samples.
+metadata : Metadata
+    Sample metadata containing formula terms.
+formula : Str
+    Model formula containing only independent terms contained in the sample
+    metadata. These can be continuous variables or factors, and they can
+    have interactions as in a typical R formula. E.g., the formula
+    "treatment+block" would test whether the input distance matrix
+    partitions based on "treatment" and "block" sample metadata. The
+    formula "treatment*block" would test both of those effects as well as
+    their interaction. Enclose formulae in quotes to avoid unpleasant
+    surprises.
+permutations : Int % Range(1, None), optional
+    The number of permutations to be run when computing p-values.
+n_jobs : Int % Range(1, None), optional
+    Number of parallel processes to run.
+
+Returns
+-------
+visualization : Visualization
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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