view qiime2/qiime_diversity_core-metrics-phylogenetic.xml @ 4:914fa4daf16a draft

Fixes

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

--i-table=$itable
--i-phylogeny=$iphylogeny
--p-sampling-depth="$psamplingdepth"

#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 + ',' + 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-faith-pd-vector=ofaithpdvector
--o-observed-otus-vector=oobservedotusvector
--o-shannon-vector=oshannonvector
--o-evenness-vector=oevennessvector
--o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix
--o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix
--o-jaccard-distance-matrix=ojaccarddistancematrix
--o-bray-curtis-distance-matrix=obraycurtisdistancematrix
--o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults
--o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults
--o-jaccard-pcoa-results=ojaccardpcoaresults
--o-bray-curtis-pcoa-results=obraycurtispcoaresults
--o-unweighted-unifrac-emperor=ounweightedunifracemperor
--o-weighted-unifrac-emperor=oweightedunifracemperor
--o-jaccard-emperor=ojaccardemperor
--o-bray-curtis-emperor=obraycurtisemperor
;
cp orarefiedtable.qza $orarefiedtable;
cp ofaithpdvector.qza $ofaithpdvector;
cp oobservedotusvector.qza $oobservedotusvector;
cp oshannonvector.qza $oshannonvector;
cp oevennessvector.qza $oevennessvector;
cp ounweightedunifracdistancematrix.qza $ounweightedunifracdistancematrix;
cp oweightedunifracdistancematrix.qza $oweightedunifracdistancematrix;
cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
cp ounweightedunifracpcoaresults.qza $ounweightedunifracpcoaresults;
cp oweightedunifracpcoaresults.qza $oweightedunifracpcoaresults;
cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
qiime tools export --input-path ounweightedunifracemperor.qzv --output-path out   && mkdir -p '$ounweightedunifracemperor.files_path'
&& cp -r out/* '$ounweightedunifracemperor.files_path'
&& mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor';
qiime tools export --input-path oweightedunifracemperor.qzv --output-path out   && mkdir -p '$oweightedunifracemperor.files_path'
&& cp -r out/* '$oweightedunifracemperor.files_path'
&& mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor';
qiime tools export --input-path ojaccardemperor.qzv --output-path out   && mkdir -p '$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 format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" 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:  (multiple arguments will be merged) The sample metadata to use in the emperor plots. [required]" name="additional_input" optional="False" 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 ${on_string}: faithpdvector.qza" name="ofaithpdvector"/>
		<data format="qza" label="${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 ${on_string}: unweightedunifracdistancematrix.qza" name="ounweightedunifracdistancematrix"/>
		<data format="qza" label="${tool.name} on ${on_string}: weightedunifracdistancematrix.qza" name="oweightedunifracdistancematrix"/>
		<data format="qza" label="${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 ${on_string}: unweightedunifracpcoaresults.qza" name="ounweightedunifracpcoaresults"/>
		<data format="qza" label="${tool.name} on ${on_string}: weightedunifracpcoaresults.qza" name="oweightedunifracpcoaresults"/>
		<data format="qza" label="${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 ${on_string}: unweightedunifracemperor.qzv" name="ounweightedunifracemperor"/>
		<data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.qzv" name="oweightedunifracemperor"/>
		<data format="html" label="${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 (phylogenetic and non-phylogenetic)
##########################################################

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

Parameters
----------
table : FeatureTable[Frequency]
    The feature table containing the samples over which diversity metrics
    should be computed.
phylogeny : Phylogeny[Rooted]
    Phylogenetic tree containing tip identifiers that correspond to the
    feature identifiers in the table. This tree can contain tip ids that
    are not present in the table, but all feature ids in the table must be
    present in this tree.
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.
faith_pd_vector : SampleData[AlphaDiversity]
    Vector of Faith PD values by sample.
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.
unweighted_unifrac_distance_matrix : DistanceMatrix
    Matrix of unweighted UniFrac distances between pairs of samples.
weighted_unifrac_distance_matrix : DistanceMatrix
    Matrix of weighted UniFrac distances between pairs of samples.
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.
unweighted_unifrac_pcoa_results : PCoAResults
    PCoA matrix computed from unweighted UniFrac distances between samples.
weighted_unifrac_pcoa_results : PCoAResults
    PCoA matrix computed from weighted UniFrac distances between 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.
unweighted_unifrac_emperor : Visualization
    Emperor plot of the PCoA matrix computed from unweighted UniFrac.
weighted_unifrac_emperor : Visualization
    Emperor plot of the PCoA matrix computed from weighted UniFrac.
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>