Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_diversity-lib_alpha-passthrough.xml @ 14:a0a8d77a991c draft
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author | florianbegusch |
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date | Thu, 03 Sep 2020 09:51:29 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_diversity-lib_alpha-passthrough.xml Thu Sep 03 09:51:29 2020 +0000 @@ -0,0 +1,88 @@ +<?xml version="1.0" ?> +<tool id="qiime_diversity-lib_alpha-passthrough" name="qiime diversity-lib alpha-passthrough" + version="2020.8"> + <description>Alpha Passthrough (non-phylogenetic)</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime diversity-lib alpha-passthrough + +--i-table=$itable + +--p-metric=$pmetric + +--o-vector=ovector + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp ovector.qza $ovector + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples for which a selected metric should be computed. [required]" name="itable" optional="False" type="data" /> + <param label="--p-metric: " name="pmetric" optional="False" type="select"> + <option value="gini_index">gini_index</option> + <option value="simpson_e">simpson_e</option> + <option value="osd">osd</option> + <option value="mcintosh_e">mcintosh_e</option> + <option value="esty_ci">esty_ci</option> + <option value="berger_parker_d">berger_parker_d</option> + <option value="robbins">robbins</option> + <option value="doubles">doubles</option> + <option value="michaelis_menten_fit">michaelis_menten_fit</option> + <option value="singles">singles</option> + <option value="kempton_taylor_q">kempton_taylor_q</option> + <option value="fisher_alpha">fisher_alpha</option> + <option value="strong">strong</option> + <option value="heip_e">heip_e</option> + <option value="dominance">dominance</option> + <option value="goods_coverage">goods_coverage</option> + <option value="ace">ace</option> + <option value="enspie">enspie</option> + <option value="mcintosh_d">mcintosh_d</option> + <option value="chao1_ci">chao1_ci</option> + <option value="lladser_pe">lladser_pe</option> + <option value="brillouin_d">brillouin_d</option> + <option value="menhinick">menhinick</option> + <option value="simpson">simpson</option> + <option value="margalef">margalef</option> + <option value="chao1">chao1</option> + </param> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: vector.qza" name="ovector" /> + + </outputs> + + <help><![CDATA[ +Alpha Passthrough (non-phylogenetic) +############################################################### + +Computes a vector of values (one value for each samples in a feature table) +using the scikit-bio implementation of the selected alpha diversity metric. + +Parameters +---------- +table : FeatureTable[Frequency] + The feature table containing the samples for which a selected metric + should be computed. +metric : Str % Choices('ace', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'michaelis_menten_fit', 'chao1_ci', 'dominance', 'robbins', 'lladser_pe', 'brillouin_d', 'goods_coverage', 'mcintosh_e', 'esty_ci', 'chao1', 'margalef', 'heip_e', 'enspie', 'menhinick', 'simpson', 'strong', 'fisher_alpha', 'osd', 'singles', 'kempton_taylor_q', 'mcintosh_d') + The alpha diversity metric to be computed. + +Returns +------- +vector : SampleData[AlphaDiversity] + Vector containing per-sample values for the chosen metric. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file