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view qiime2/qiime_diversity_alpha.xml @ 7:85b520815e85 draft
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author | florianbegusch |
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date | Tue, 13 Aug 2019 07:53:59 -0400 |
parents | 370e0b6e9826 |
children | f190567fe3f6 |
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<?xml version="1.0" ?> <tool id="qiime_diversity_alpha" name="qiime diversity alpha" version="2019.4"> <description> - Alpha diversity</description> <requirements> <requirement type="package" version="2019.4">qiime2</requirement> </requirements> <command><![CDATA[ qiime diversity alpha --i-table=$itable --p-metric=$pmetric --o-alpha-diversity=oalphadiversity ; cp oalphadiversity.qza $oalphadiversity ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed. [required]" name="itable" optional="False" type="data"/> <param label="--p-metric: " name="pmetric" optional="False" type="select"> <option value="menhinick">menhinick</option> <option value="gini_index">gini_index</option> <option value="chao1_ci">chao1_ci</option> <option value="lladser_pe">lladser_pe</option> <option value="observed_otus">observed_otus</option> <option value="lladser_ci">lladser_ci</option> <option value="simpson_e">simpson_e</option> <option value="shannon">shannon</option> <option value="pielou_e">pielou_e</option> <option value="heip_e">heip_e</option> <option value="mcintosh_e">mcintosh_e</option> <option value="osd">osd</option> <option value="fisher_alpha">fisher_alpha</option> <option value="goods_coverage">goods_coverage</option> <option value="strong">strong</option> <option value="simpson">simpson</option> <option value="dominance">dominance</option> <option value="ace">ace</option> <option value="brillouin_d">brillouin_d</option> <option value="margalef">margalef</option> <option value="esty_ci">esty_ci</option> <option value="kempton_taylor_q">kempton_taylor_q</option> <option value="berger_parker_d">berger_parker_d</option> <option value="enspie">enspie</option> <option value="doubles">doubles</option> <option value="robbins">robbins</option> <option value="singles">singles</option> <option value="mcintosh_d">mcintosh_d</option> <option value="chao1">chao1</option> <option value="michaelis_menten_fit">michaelis_menten_fit</option> </param> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: alphadiversity.qza" name="oalphadiversity"/> </outputs> <help><![CDATA[ Alpha diversity ############### Computes a user-specified alpha diversity metric for all samples in a feature table. Parameters ---------- table : FeatureTable[Frequency] The feature table containing the samples for which alpha diversity should be computed. metric : Str % Choices('pielou_e', 'menhinick', 'mcintosh_e', 'doubles', 'chao1_ci', 'kempton_taylor_q', 'enspie', 'heip_e', 'michaelis_menten_fit', 'observed_otus', 'gini_index', 'dominance', 'osd', 'esty_ci', 'ace', 'berger_parker_d', 'lladser_ci', 'simpson_e', 'shannon', 'margalef', 'brillouin_d', 'robbins', 'simpson', 'fisher_alpha', 'singles', 'goods_coverage', 'mcintosh_d', 'chao1', 'lladser_pe', 'strong') The alpha diversity metric to be computed. Returns ------- alpha_diversity : SampleData[AlphaDiversity] Vector containing per-sample alpha diversities. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>