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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:55:05 +0000 |
parents | d93d8888f0b0 |
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<?xml version="1.0" ?> <tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic" version="2020.8"> <description>Core diversity metrics (phylogenetic and non- phylogenetic)</description> <requirements> <requirement type="package" version="2020.8">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity core-metrics-phylogenetic --i-table=$itable --i-phylogeny=$iphylogeny --p-sampling-depth=$psamplingdepth # 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($input_files_mmetadatafile) # end if #if str($pnjobsorthreads) != 'None': --p-n-jobs-or-threads=$pnjobsorthreads #end if --o-rarefied-table=orarefiedtable --o-faith-pd-vector=ofaithpdvector --o-observed-features-vector=oobservedfeaturesvector --o-shannon-vector=oshannonvector --o-evenness-vector=oevennessvector --o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix --o-jaccard-distance-matrix=ojaccarddistancematrix --o-bray-curtis-distance-matrix=obraycurtisdistancematrix --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults --o-jaccard-pcoa-results=ojaccardpcoaresults --o-bray-curtis-pcoa-results=obraycurtispcoaresults --o-unweighted-unifrac-emperor=ounweightedunifracemperor --o-weighted-unifrac-emperor=oweightedunifracemperor --o-jaccard-emperor=ojaccardemperor --o-bray-curtis-emperor=obraycurtisemperor #if str($examples) != 'None': --examples=$examples #end if ; cp obraycurtispcoaresults.qza $obraycurtispcoaresults ; qiime tools export ounweightedunifracemperor.qzv --output-path out && mkdir -p '$ounweightedunifracemperor.files_path' && cp -r out/* '$ounweightedunifracemperor.files_path' && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor' ; qiime tools export oweightedunifracemperor.qzv --output-path out && mkdir -p '$oweightedunifracemperor.files_path' && cp -r out/* '$oweightedunifracemperor.files_path' && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor' ; qiime tools export ojaccardemperor.qzv --output-path out && mkdir -p '$ojaccardemperor.files_path' && cp -r out/* '$ojaccardemperor.files_path' && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor' ; qiime tools export obraycurtisemperor.qzv --output-path out && mkdir -p '$obraycurtisemperor.files_path' && cp -r out/* '$obraycurtisemperor.files_path' && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor' ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data" /> <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT Phylogenetic tree containing tip identifiers that Phylogeny[Rooted] correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="iphylogeny" optional="False" type="data" /> <param label="--p-sampling-depth: INTEGER Range(1, None) The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text" /> <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file"> <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple arguments The sample metadata to use in the emperor plots. will be merged) [required]" name="additional_input" optional="False" type="data" /> </repeat> <param label="--p-n-jobs-or-threads: " name="pnjobsorthreads" optional="True" type="select"> <option selected="True" value="None">Selection is Optional</option> <option value="Int % Range(1">Int % Range(1</option> <option value="None">None</option> </param> <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> </inputs> <outputs> <data format="qza" label="${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 ${on_string}: observedfeaturesvector.qza" name="oobservedfeaturesvector" /> <data format="qza" label="${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 ${on_string}: unweightedunifracemperor.html" name="ounweightedunifracemperor" /> <data format="html" label="${tool.name} on ${on_string}: weightedunifracemperor.html" name="oweightedunifracemperor" /> <data format="html" label="${tool.name} on ${on_string}: jaccardemperor.html" name="ojaccardemperor" /> <data format="html" label="${tool.name} on ${on_string}: braycurtisemperor.html" 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. n_jobs_or_threads : Int % Range(1, None) | Str % Choices('auto'), optional [beta/beta-phylogenetic methods only] - The number of concurrent jobs or CPU threads to use in performing this calculation. Individual methods will create jobs/threads as implemented in q2-diversity-lib dependencies. May not exceed the number of available physical cores. If n_jobs_or_threads = 'auto', one thread/job will be created for each identified CPU core on the host. Returns ------- rarefied_table : FeatureTable[Frequency] The resulting rarefied feature table. faith_pd_vector : SampleData[AlphaDiversity] Vector of Faith PD values by sample. observed_features_vector : SampleData[AlphaDiversity] Vector of Observed Features 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>