view qiime2/qiime_longitudinal_plot-feature-volatility.xml @ 8:d66c7509e8f9 draft

Uploaded

<?xml version="1.0" ?>
<tool id="qiime_longitudinal_plot-feature-volatility" name="qiime longitudinal plot-feature-volatility" version="2019.4">
	<description> - Plot longitudinal feature volatility and importances</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime longitudinal plot-feature-volatility

--i-table=$itable
--i-importances=$iimportances
--p-state-column="$pstatecolumn"



#if '__sq__' in str($pindividualidcolumn):
  #set $pindividualidcolumn_temp = $pindividualidcolumn.replace('__sq__', "'")
  #set $pindividualidcolumn = $pindividualidcolumn_temp
#end if

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




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

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


--o-visualization=ovisualization
;
qiime tools export --input-path 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"/>
		<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="True" 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="True" 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>

		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file  [required]">
			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" 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 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.

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