annotate qiime2/qiime_diversity_core-metrics.xml @ 6:de4c22a52df4 draft

Fixes

<?xml version="1.0" ?>
<tool id="qiime_diversity_core-metrics" name="qiime diversity core-metrics" version="2019.4">
	<description> - Core diversity metrics (non-phylogenetic)</description>
	<requirements>
		<requirement type="package" version="2019.4">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime diversity core-metrics

--i-table=$itable

#if str($psamplingdepth):
 --p-sampling-depth="$psamplingdepth"
#end if

#set $pnjobs = '${GALAXY_SLOTS:-4}'
#if str($pnjobs):
 --p-n-jobs="$pnjobs"
#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-rarefied-table=orarefiedtable
--o-observed-otus-vector=oobservedotusvector
--o-shannon-vector=oshannonvector
--o-evenness-vector=oevennessvector
--o-jaccard-distance-matrix=ojaccarddistancematrix
--o-bray-curtis-distance-matrix=obraycurtisdistancematrix
--o-jaccard-pcoa-results=ojaccardpcoaresults
--o-bray-curtis-pcoa-results=obraycurtispcoaresults
--o-jaccard-emperor=ojaccardemperor
--o-bray-curtis-emperor=obraycurtisemperor
;
cp orarefiedtable.qza $orarefiedtable;
cp oobservedotusvector.qza $oobservedotusvector;
cp oshannonvector.qza $oshannonvector;
cp oevennessvector.qza $oevennessvector;
cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
qiime tools export --input-path ojaccardemperor.qzv --output-path out   && mkdir -p '$ojaccardemperor.files_path'
&& cp -r out/* '$ojaccardemperor.files_path'
&& mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
qiime tools export --input-path obraycurtisemperor.qzv --output-path out   && mkdir -p '$obraycurtisemperor.files_path'
&& cp -r out/* '$obraycurtisemperor.files_path'
&& mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
	]]></command>
	<inputs>
		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed.        [required]" name="itable" optional="False" type="data"/>
		<param label="--p-sampling-depth: INTEGER Range(1, None)     The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" min="1" value="" type="integer"/>

		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file  [required]">
			<param label="--m-metadata-file: METADATA... (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
		</repeat>

	</inputs>
	<outputs>
		<data format="qza" label="${tool.name} on ${on_string}: rarefiedtable.qza" name="orarefiedtable"/>
		<data format="qza" label="${tool.name} on ${on_string}: observedotusvector.qza" name="oobservedotusvector"/>
		<data format="qza" label="${tool.name} on ${on_string}: shannonvector.qza" name="oshannonvector"/>
		<data format="qza" label="${tool.name} on ${on_string}: evennessvector.qza" name="oevennessvector"/>
		<data format="qza" label="${tool.name} on ${on_string}: jaccarddistancematrix.qza" name="ojaccarddistancematrix"/>
		<data format="qza" label="${tool.name} on ${on_string}: braycurtisdistancematrix.qza" name="obraycurtisdistancematrix"/>
		<data format="qza" label="${tool.name} on ${on_string}: jaccardpcoaresults.qza" name="ojaccardpcoaresults"/>
		<data format="qza" label="${tool.name} on ${on_string}: braycurtispcoaresults.qza" name="obraycurtispcoaresults"/>
		<data format="html" label="${tool.name} on ${on_string}: jaccardemperor.qzv" name="ojaccardemperor"/>
		<data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.qzv" name="obraycurtisemperor"/>
	</outputs>
	<help><![CDATA[
Core diversity metrics (non-phylogenetic)
#########################################

Applies a collection of diversity metrics (non-phylogenetic) to a feature
table.

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples over which diversity metrics
    should be computed.
sampling_depth : Int % Range(1, None)
    The total frequency that each sample should be rarefied to prior to
    computing diversity metrics.
metadata : Metadata
    The sample metadata to use in the emperor plots.

Returns
-------
rarefied_table : FeatureTable[Frequency]
    The resulting rarefied feature table.
observed_otus_vector : SampleData[AlphaDiversity]
    Vector of Observed OTUs values by sample.
shannon_vector : SampleData[AlphaDiversity]
    Vector of Shannon diversity values by sample.
evenness_vector : SampleData[AlphaDiversity]
    Vector of Pielou's evenness values by sample.
jaccard_distance_matrix : DistanceMatrix
    Matrix of Jaccard distances between pairs of samples.
bray_curtis_distance_matrix : DistanceMatrix
    Matrix of Bray-Curtis distances between pairs of samples.
jaccard_pcoa_results : PCoAResults
    PCoA matrix computed from Jaccard distances between samples.
bray_curtis_pcoa_results : PCoAResults
    PCoA matrix computed from Bray-Curtis distances between samples.
jaccard_emperor : Visualization
    Emperor plot of the PCoA matrix computed from Jaccard.
bray_curtis_emperor : Visualization
    Emperor plot of the PCoA matrix computed from Bray-Curtis.
	]]></help>
<macros>
    <import>qiime_citation.xml</import>
</macros>
<expand macro="qiime_citation"/>
</tool>