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+++ b/qiime2-2020.8/qiime_diversity_beta-correlation.xml	Thu Sep 03 09:33:04 2020 +0000
@@ -0,0 +1,160 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity_beta-correlation" name="qiime diversity beta-correlation"
+      version="2020.8">
+  <description>Beta diversity correlation</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime diversity beta-correlation
+
+--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
+
+--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# if $input_files_ometadatadistancematrix:
+  # 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 + ' --o-metadata-distance-matrix=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--o-metadata-distance-matrix=$list_dict_to_string($input_files_ometadatadistancematrix)
+# end if
+
+--o-mantel-scatter-visualization=omantelscattervisualization
+
+#if str($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'
+
+  ]]></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[Numeric] Numeric metadata column from which to compute pairwise Euclidean distances                          [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="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 `distance-matrix` in the output visualization.                    [default: \'Metadata\']" name="plabel1" optional="False" type="text" value="\'Metadata\'" />
+    <param label="--p-label2: TEXT      Label for `metadata-distance-matrix` in the output visualization.             [default: \'Distance Matrix\']" name="plabel2" optional="False" type="text" value="\'Distance Matrix\'" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <repeat name="input_files_ometadatadistancematrix" optional="False" title="--o-metadata-distance-matrix">
+      <param format="tabular,qza,no_unzip.zip" label="--o-metadata-distance-matrix: ARTIFACT DistanceMatrix     The Distance Matrix produced from the metadata column and used in the mantel test                  [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <data format="html" label="${tool.name} on ${on_string}: mantelscattervisualization.html" name="omantelscattervisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Beta diversity correlation
+###############################################################
+
+Create a distance matrix from a numeric metadata column and apply a two-
+sided Mantel test to identify correlation between two distance matrices.
+Actions used internally: `distance-matrix` from q2-metadata and `mantel`
+from q2-diversity.
+
+Parameters
+----------
+metadata : MetadataColumn[Numeric]
+    Numeric metadata column from which to compute pairwise Euclidean
+    distances
+distance_matrix : 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 `distance_matrix` in the output visualization.
+label2 : Str, optional
+    Label for `metadata_distance_matrix` in the output visualization.
+
+Returns
+-------
+metadata_distance_matrix : DistanceMatrix
+    The Distance Matrix produced from the metadata column and used in the
+    mantel test
+mantel_scatter_visualization : Visualization
+    Scatter plot rendering of the manteltest results
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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