annotate qiime2-2020.8/qiime_diversity_core-metrics-phylogenetic.xml @ 20:d93d8888f0b0 draft

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<?xml version="1.0" ?>
<tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic"
      version="2020.8">
  <description>Core diversity metrics (phylogenetic and non- phylogenetic)</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime diversity core-metrics-phylogenetic

--i-table=$itable

--i-phylogeny=$iphylogeny

--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 str($pnjobsorthreads) != 'None':
--p-n-jobs-or-threads=$pnjobsorthreads
#end if

--o-rarefied-table=orarefiedtable

--o-faith-pd-vector=ofaithpdvector

--o-observed-features-vector=oobservedfeaturesvector

--o-shannon-vector=oshannonvector

--o-evenness-vector=oevennessvector

--o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix

--o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix

--o-jaccard-distance-matrix=ojaccarddistancematrix

--o-bray-curtis-distance-matrix=obraycurtisdistancematrix

--o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults

--o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults

--o-jaccard-pcoa-results=ojaccardpcoaresults

--o-bray-curtis-pcoa-results=obraycurtispcoaresults

--o-unweighted-unifrac-emperor=ounweightedunifracemperor

--o-weighted-unifrac-emperor=oweightedunifracemperor

--o-jaccard-emperor=ojaccardemperor

--o-bray-curtis-emperor=obraycurtisemperor

#if str($examples) != 'None':
--examples=$examples
#end if

;
cp obraycurtispcoaresults.qza $obraycurtispcoaresults

;
qiime tools export  ounweightedunifracemperor.qzv --output-path out
&& mkdir -p '$ounweightedunifracemperor.files_path'
&& cp -r out/* '$ounweightedunifracemperor.files_path'
&& mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor'

;
qiime tools export  oweightedunifracemperor.qzv --output-path out
&& mkdir -p '$oweightedunifracemperor.files_path'
&& cp -r out/* '$oweightedunifracemperor.files_path'
&& mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor'

;
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 format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" 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 arguments   The sample metadata to use in the emperor plots. will be merged)                                                [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param label="--p-n-jobs-or-threads: " name="pnjobsorthreads" 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 ${on_string}: faithpdvector.qza" name="ofaithpdvector" />
    <data format="qza" label="${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 ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix" />
    <data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix" />
    <data format="qza" label="${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 ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults" />
    <data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults" />
    <data format="qza" label="${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 ${on_string}: unweightedunifracemperor.html" name="ounweightedunifracemperor" />
    <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.html" name="oweightedunifracemperor" />
    <data format="html" label="${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 (phylogenetic and non- phylogenetic)
###############################################################

Applies a collection of diversity metrics (both phylogenetic and non-
phylogenetic) to a feature table.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples over which diversity metrics
    should be computed.
phylogeny : Phylogeny[Rooted]
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
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.
n_jobs_or_threads : Int % Range(1, None) | Str % Choices('auto'), optional
    [beta/beta-phylogenetic methods only] - The number of concurrent jobs
    or CPU threads to use in performing this calculation. Individual
    methods will create jobs/threads as implemented in q2-diversity-lib
    dependencies. May not exceed the number of available physical cores. If
    n_jobs_or_threads = 'auto', one thread/job will be created for each
    identified CPU core on the host.

Returns
-------
rarefied_table : FeatureTable[Frequency]
    The resulting rarefied feature table.
faith_pd_vector : SampleData[AlphaDiversity]
    Vector of Faith PD values by sample.
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.
unweighted_unifrac_distance_matrix : DistanceMatrix
    Matrix of unweighted UniFrac distances between pairs of samples.
weighted_unifrac_distance_matrix : DistanceMatrix
    Matrix of weighted UniFrac distances between pairs of samples.
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.
unweighted_unifrac_pcoa_results : PCoAResults
    PCoA matrix computed from unweighted UniFrac distances between samples.
weighted_unifrac_pcoa_results : PCoAResults
    PCoA matrix computed from weighted UniFrac distances between 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.
unweighted_unifrac_emperor : Visualization
    Emperor plot of the PCoA matrix computed from unweighted UniFrac.
weighted_unifrac_emperor : Visualization
    Emperor plot of the PCoA matrix computed from weighted UniFrac.
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>