annotate qiime2/qiime_longitudinal_volatility.xml @ 14:a0a8d77a991c draft

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<?xml version="1.0" ?>
<tool id="qiime_longitudinal_volatility" name="qiime longitudinal volatility"
      version="2020.8">
  <description>Generate interactive volatility plot</description>
  <requirements>
    <requirement type="package" version="2020.8">qiime2</requirement>
  </requirements>
  <command><![CDATA[
qiime longitudinal volatility

#if str($itable) != 'None':
--i-table=$itable
#end if
# 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($pdefaultmetric):
  --p-default-metric=$pdefaultmetric
#end if
#if str($pyscale) != 'None':
--p-yscale=$pyscale
#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'

;
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 metrics.          [optional]" name="itable" 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-default-metric: TEXT Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization).           [optional]" name="pdefaultmetric" 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="--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[
Generate interactive volatility plot
###############################################################

Generate an interactive control chart depicting the longitudinal volatility
of sample metadata and/or feature frequencies across time (as set using the
"state_column" parameter). Any numeric metadata column (and metadata-
transformable artifacts, e.g., alpha diversity results) can be plotted on
the y-axis, and are selectable using the "metric_column" selector. Metric
values are averaged to compare across any categorical metadata column using
the "group_column" selector. Longitudinal volatility for individual
subjects sampled over time is co-plotted as "spaghetti" plots if the
"individual_id_column" parameter is used. state_column will typically be a
measure of time, but any numeric metadata column can be used.

Parameters
----------
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).
default_metric : Str, optional
    Numeric metadata or artifact column to test by default (all numeric
    metadata columns will be available in the visualization).
table : FeatureTable[RelativeFrequency], optional
    Feature table containing metrics.
yscale : Str % Choices('linear', 'pow', 'sqrt', 'log'), optional
    y-axis scaling strategy to apply.

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