comparison qiime2/qiime_diversity_core-metrics.xml @ 29:3ba9833030c1 draft

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29:3ba9833030c1

<?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>