view qiime2/qiime_diversity_alpha-rarefaction.xml @ 0:370e0b6e9826 draft

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<?xml version="1.0" ?>
<tool id="qiime_diversity_alpha-rarefaction" name="qiime diversity alpha-rarefaction" version="2019.4">
	<description> - Alpha rarefaction curves</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime diversity alpha-rarefaction

--i-table=$itable
--p-max-depth="$pmaxdepth"

#if str($iphylogeny) != 'None':
 --i-phylogeny=$iphylogeny
#end if

#if str($pmetrics) != 'None':
 --p-metrics=$pmetrics
#end if


#if $pmindepth:
 --p-min-depth=$pmindepth
#end if

#if $psteps:
 --p-steps=$psteps
#end if

#if $piterations:
 --p-iterations=$piterations
#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 + ',' + 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[Frequency] Feature table to compute rarefaction curves from. [required]" name="itable" optional="False" type="data"/>
		<param label="--p-max-depth: INTEGER   The maximum rarefaction depth. Must be greater than Range(1, None)        min-depth.                                [required]" name="pmaxdepth" optional="False" min="1" value="" type="integer"/>
		<param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Optional phylogeny for phylogenetic metrics. Phylogeny[Rooted]                                               [optional]" name="iphylogeny" optional="True" type="data"/>
		<param label="--p-metrics: " name="pmetrics" optional="True" type="select">
			<option selected="True" value="None">Selection is Optional</option>
			<option value="dominance">dominance</option>
			<option value="ace">ace</option>
			<option value="brillouin_d">brillouin_d</option>
			<option value="margalef">margalef</option>
			<option value="menhinick">menhinick</option>
			<option value="mcintosh_d">mcintosh_d</option>
			<option value="berger_parker_d">berger_parker_d</option>
			<option value="enspie">enspie</option>
			<option value="doubles">doubles</option>
			<option value="lladser_pe">lladser_pe</option>
			<option value="observed_otus">observed_otus</option>
			<option value="faith_pd">faith_pd</option>
			<option value="simpson_e">simpson_e</option>
			<option value="robbins">robbins</option>
			<option value="shannon">shannon</option>
			<option value="pielou_e">pielou_e</option>
			<option value="singles">singles</option>
			<option value="michaelis_menten_fit">michaelis_menten_fit</option>
			<option value="heip_e">heip_e</option>
			<option value="mcintosh_e">mcintosh_e</option>
			<option value="fisher_alpha">fisher_alpha</option>
			<option value="goods_coverage">goods_coverage</option>
			<option value="chao1">chao1</option>
			<option value="gini_index">gini_index</option>
			<option value="simpson">simpson</option>
		</param>
		<param label="--p-min-depth: INTEGER   The minimum rarefaction depth. Range(1, None)                                                [default: 1]" name="pmindepth" optional="True" type="integer" min="1" value="1"/>
		<param label="--p-steps: INTEGER       The number of rarefaction depths to include between Range(2, None)        min-depth and max-depth.               [default: 10]" name="psteps" optional="True" type="integer" min="2" value="10"/>
		<param label="--p-iterations: INTEGER  The number of rarefied feature tables to compute at Range(1, None)        each step.                             [default: 10]" name="piterations" optional="True" type="integer" min="1" value="10"/>

		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample 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[
Alpha rarefaction curves
########################

Generate interactive alpha rarefaction curves by computing rarefactions
between `min_depth` and `max_depth`. The number of intermediate depths to
compute is controlled by the `steps` parameter, with n `iterations` being
computed at each rarefaction depth. If sample metadata is provided, samples
may be grouped based on distinct values within a metadata column.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table to compute rarefaction curves from.
max_depth : Int % Range(1, None)
    The maximum rarefaction depth. Must be greater than min_depth.
phylogeny : Phylogeny[Rooted], optional
    Optional phylogeny for phylogenetic metrics.
metrics : Set[Str % Choices('pielou_e', 'simpson_e', 'shannon', 'margalef', 'menhinick', 'brillouin_d', 'mcintosh_e', 'doubles', 'robbins', 'simpson', 'enspie', 'fisher_alpha', 'heip_e', 'singles', 'michaelis_menten_fit', 'observed_otus', 'gini_index', 'dominance', 'goods_coverage', 'mcintosh_d', 'faith_pd', 'ace', 'chao1', 'lladser_pe', 'berger_parker_d')], optional
    The metrics to be measured. By default computes observed_otus, shannon,
    and if phylogeny is provided, faith_pd.
metadata : Metadata, optional
    The sample metadata.
min_depth : Int % Range(1, None), optional
    The minimum rarefaction depth.
steps : Int % Range(2, None), optional
    The number of rarefaction depths to include between min_depth and
    max_depth.
iterations : Int % Range(1, None), optional
    The number of rarefied feature tables to compute at each step.

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