view qiime2/qiime_composition_ancom.xml @ 6:de4c22a52df4 draft

Fixes

<?xml version="1.0" ?>
<tool id="qiime_composition_ancom" name="qiime composition ancom" version="2019.4">
	<description> - Apply ANCOM to identify features that differ in abundance.</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime composition ancom

--i-table=$itable



#if $metadatafile:
 --m-metadata-file=$metadatafile
#end if



--m-metadata-column="$mmetadatacolumn"

#if str($pdifferencefunction) != 'None':
--p-difference-function=$pdifferencefunction
#end if

#if str($ptransformfunction) != 'None':
--p-transform-function=$ptransformfunction
#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: FeatureTable[Composition] - The feature table to be used for ANCOM computation.  [required]" name="itable" optional="False" type="data"/>

		<param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" optional="True" />


		<param label="--m-metadata-column: MetadataColumn[Categorical] - Column from metadata file or artifact viewable as metadata. The categorical sample metadata column to test for differential abundance across.  [required]" name="mmetadatacolumn" optional="False" type="text"/>
		<param label="--p-difference-function: " name="pdifferencefunction" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="mean_difference">mean_difference</option>
			<option value="f_statistic">f_statistic</option>
		</param>
		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
		<param label="--p-transform-function: " name="ptransformfunction" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="log">log</option>
			<option value="clr">clr</option>
			<option value="sqrt">sqrt</option>
		</param>
	</inputs>
	<outputs>
		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
	</outputs>
	<help><![CDATA[
Apply ANCOM to identify features that differ in abundance.
##########################################################

Apply Analysis of Composition of Microbiomes (ANCOM) to identify features
that are differentially abundant across groups.

Parameters
----------
table : FeatureTable[Composition]
    The feature table to be used for ANCOM computation.
metadata : MetadataColumn[Categorical]
    The categorical sample metadata column to test for differential
    abundance across.
transform_function : Str % Choices('sqrt', 'log', 'clr'), optional
    The method applied to transform feature values before generating
    volcano plots.
difference_function : Str % Choices('mean_difference', 'f_statistic'), optional
    The method applied to visualize fold difference in feature abundances
    across groups for volcano plots.

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