view qiime2/qiime_longitudinal_plot-feature-volatility.xml @ 29:3ba9833030c1 draft

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<?xml version="1.0" ?>
<tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility"
      version="2020.8">
  <description>Plot longitudinal feature volatility and importances</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime longitudinal plot-feature-volatility

--i-table=$itable

--i-importances=$iimportances
# 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($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__ob__', '[')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__cb__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__cb__', ']')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if 'X' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('X', '\\')
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__sq__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__sq__', "'")
  #set $pstatecolumn = $pstatecolumn_temp
#end if
#if '__db__' in str($pstatecolumn):
  #set $pstatecolumn_temp = $pstatecolumn.replace('__db__', '"')
  #set $pstatecolumn = $pstatecolumn_temp
#end if

--p-state-column=$pstatecolumn


#if '__ob__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__ob__', '[')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__cb__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__cb__', ']')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if 'X' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('X', '\\')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__sq__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if
#if '__db__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__db__', '"')
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if

#if str($pindividualidcolumn):
  --p-individual-id-column=$pindividualidcolumn
#end if

#if '__ob__' in str($pdefaultgroupcolumn):
  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__ob__', '[')
  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
#end if
#if '__cb__' in str($pdefaultgroupcolumn):
  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__cb__', ']')
  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
#end if
#if 'X' in str($pdefaultgroupcolumn):
  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('X', '\\')
  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
#end if
#if '__sq__' in str($pdefaultgroupcolumn):
  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__sq__', "'")
  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
#end if
#if '__db__' in str($pdefaultgroupcolumn):
  #set $pdefaultgroupcolumn_temp = $pdefaultgroupcolumn.replace('__db__', '"')
  #set $pdefaultgroupcolumn = $pdefaultgroupcolumn_temp
#end if

#if str($pdefaultgroupcolumn):
  --p-default-group-column=$pdefaultgroupcolumn
#end if

#if str($pyscale) != 'None':
--p-yscale=$pyscale
#end if

#if str($pimportancethreshold) != 'None':
--p-importance-threshold=$pimportancethreshold
#end if

#if str($pfeaturecount) != 'None':
--p-feature-count=$pfeaturecount
#end if

#if str($pmissingsamples) != 'None':
--p-missing-samples=$pmissingsamples
#end if

--o-visualization=ovisualization

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

;
cp odistancematrix.qza $odistancematrix

;
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'

;
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-table: ARTIFACT FeatureTable[RelativeFrequency] Feature table containing features found in importances.                               [required]" name="itable" optional="False" type="data" />
    <param format="qza,no_unzip.zip" label="--i-importances: ARTIFACT FeatureData[Importance] Feature importance scores.                 [required]" name="iimportances" 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 file containing arguments will be   individual-id-column. merged)                                                        [required]" name="additional_input" optional="False" type="data" />
    </repeat>
    <param label="--p-state-column: TEXT  Metadata column containing state (time) variable information.                               [required]" name="pstatecolumn" optional="False" type="text" />
    <param label="--p-individual-id-column: TEXT Metadata column containing IDs for individual subjects.                                  [optional]" name="pindividualidcolumn" optional="False" type="text" />
    <param label="--p-default-group-column: TEXT The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization). [optional]" name="pdefaultgroupcolumn" optional="False" type="text" />
    <param label="--p-yscale: " name="pyscale" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="linear">linear</option>
      <option value="pow">pow</option>
      <option value="sqrt">sqrt</option>
      <option value="log">log</option>
    </param>
    <param label="--p-importance-threshold: " name="pimportancethreshold" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="Float % Range(0">Float % Range(0</option>
      <option value="None">None</option>
      <option value="inclusive_start=False">inclusive_start=False</option>
    </param>
    <param label="--p-feature-count: " name="pfeaturecount" 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="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
      <option selected="True" value="None">Selection is Optional</option>
      <option value="error">error</option>
      <option value="ignore">ignore</option>
    </param>
    <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[
Plot longitudinal feature volatility and importances
###############################################################

Plots an interactive control chart of feature abundances (y-axis) in each
sample across time (or state; x-axis). Feature importance scores and
descriptive statistics for each feature are plotted in interactive bar
charts below the control chart, facilitating exploration of longitudinal
feature data. This visualization is intended for use with the feature-
volatility pipeline; use that pipeline to access this visualization.

Parameters
----------
table : FeatureTable[RelativeFrequency]
    Feature table containing features found in importances.
importances : FeatureData[Importance]
    Feature importance scores.
metadata : Metadata
    Sample metadata file containing individual_id_column.
state_column : Str
    Metadata column containing state (time) variable information.
individual_id_column : Str, optional
    Metadata column containing IDs for individual subjects.
default_group_column : Str, optional
    The default metadata column on which to separate groups for comparison
    (all categorical metadata columns will be available in the
    visualization).
yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
    y-axis scaling strategy to apply.
importance_threshold : Float % Range(0, None, inclusive_start=False) | Str % Choices('q1', 'q2', 'q3'), optional
    Filter feature table to exclude any features with an importance score
    less than this threshold. Set to "q1", "q2", or "q3" to select the
    first, second, or third quartile of values. Set to "None" to disable
    this filter.
feature_count : Int % Range(1, None) | Str % Choices('all'), optional
    Filter feature table to include top N most important features. Set to
    "all" to include all features.
missing_samples : Str % Choices('error', 'ignore'), optional
    How to handle missing samples in metadata. "error" will fail if missing
    samples are detected. "ignore" will cause the feature table and
    metadata to be filtered, so that only samples found in both files are
    retained.

Returns
-------
visualization : Visualization
  ]]></help>
  <macros>
    <import>qiime_citation.xml</import>
  </macros>
  <expand macro="qiime_citation"/>
</tool>