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+++ b/qiime2-2020.8/qiime_diversity_core-metrics.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,156 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics"
+      version="2020.8">
+  <description>Core diversity metrics (non-phylogenetic)</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime diversity core-metrics
+
+--i-table=$itable
+
+--p-sampling-depth=$psamplingdepth
+# 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 $pwithreplacement:
+ --p-with-replacement
+#end if
+
+#if str($pnjobs) != 'None':
+--p-n-jobs=$pnjobs
+#end if
+
+--o-rarefied-table=orarefiedtable
+
+--o-observed-features-vector=oobservedfeaturesvector
+
+--o-shannon-vector=oshannonvector
+
+--o-evenness-vector=oevennessvector
+
+--o-jaccard-distance-matrix=ojaccarddistancematrix
+
+--o-bray-curtis-distance-matrix=obraycurtisdistancematrix
+
+--o-jaccard-pcoa-results=ojaccardpcoaresults
+
+--o-bray-curtis-pcoa-results=obraycurtispcoaresults
+
+--o-jaccard-emperor=ojaccardemperor
+
+--o-bray-curtis-emperor=obraycurtisemperor
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp obraycurtispcoaresults.qza $obraycurtispcoaresults
+
+;
+qiime tools export  ojaccardemperor.qzv --output-path out
+&& mkdir -p '$ojaccardemperor.files_path'
+&& cp -r out/* '$ojaccardemperor.files_path'
+&& mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor'
+
+;
+qiime tools export  obraycurtisemperor.qzv --output-path out
+&& mkdir -p '$obraycurtisemperor.files_path'
+&& cp -r out/* '$obraycurtisemperor.files_path'
+&& mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed.        [required]" name="itable" optional="False" type="data" />
+    <param label="--p-sampling-depth: INTEGER Range(1, None)     The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple          The sample metadata to use in the emperor plots. arguments will be merged)                                                     [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--p-with-replacement: --p-with-replacement: / --p-no-with-replacement Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement.                           [default: False]" name="pwithreplacement" selected="False" type="boolean" />
+    <param label="--p-n-jobs: " name="pnjobs" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Int % Range(1">Int % Range(1</option>
+      <option value="None">None</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable" />
+    <data format="qza" label="${tool.name} on ${on_string}: observedfeaturesvector.qza" name="oobservedfeaturesvector" />
+    <data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector" />
+    <data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector" />
+    <data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix" />
+    <data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix" />
+    <data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults" />
+    <data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults" />
+    <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.html" name="ojaccardemperor" />
+    <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.html" name="obraycurtisemperor" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Core diversity metrics (non-phylogenetic)
+###############################################################
+
+Applies a collection of diversity metrics (non-phylogenetic) to a feature
+table.
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    The feature table containing the samples over which diversity metrics
+    should be computed.
+sampling_depth : Int % Range(1, None)
+    The total frequency that each sample should be rarefied to prior to
+    computing diversity metrics.
+metadata : Metadata
+    The sample metadata to use in the emperor plots.
+with_replacement : Bool, optional
+    Rarefy with replacement by sampling from the multinomial distribution
+    instead of rarefying without replacement.
+n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
+    [beta methods only] - The number of concurrent jobs to use in
+    performing this calculation. May not exceed the number of available
+    physical cores. If n_jobs = 'auto', one job will be launched for each
+    identified CPU core on the host.
+
+Returns
+-------
+rarefied_table : FeatureTable[Frequency]
+    The resulting rarefied feature table.
+observed_features_vector : SampleData[AlphaDiversity]
+    Vector of Observed Features values by sample.
+shannon_vector : SampleData[AlphaDiversity]
+    Vector of Shannon diversity values by sample.
+evenness_vector : SampleData[AlphaDiversity]
+    Vector of Pielou's evenness values by sample.
+jaccard_distance_matrix : DistanceMatrix
+    Matrix of Jaccard distances between pairs of samples.
+bray_curtis_distance_matrix : DistanceMatrix
+    Matrix of Bray-Curtis distances between pairs of samples.
+jaccard_pcoa_results : PCoAResults
+    PCoA matrix computed from Jaccard distances between samples.
+bray_curtis_pcoa_results : PCoAResults
+    PCoA matrix computed from Bray-Curtis distances between samples.
+jaccard_emperor : Visualization
+    Emperor plot of the PCoA matrix computed from Jaccard.
+bray_curtis_emperor : Visualization
+    Emperor plot of the PCoA matrix computed from Bray-Curtis.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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