Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_diversity_alpha.xml @ 14:a0a8d77a991c draft
Uploaded
author | florianbegusch |
---|---|
date | Thu, 03 Sep 2020 09:51:29 +0000 |
parents | f190567fe3f6 |
children |
line wrap: on
line diff
--- a/qiime2/qiime_diversity_alpha.xml Thu Sep 03 09:46:00 2020 +0000 +++ b/qiime2/qiime_diversity_alpha.xml Thu Sep 03 09:51:29 2020 +0000 @@ -1,79 +1,91 @@ <?xml version="1.0" ?> -<tool id="qiime_diversity_alpha" name="qiime diversity alpha" version="2019.7"> - <description> - Alpha diversity</description> - <requirements> - <requirement type="package" version="2019.7">qiime2</requirement> - </requirements> - <command><![CDATA[ +<tool id="qiime_diversity_alpha" name="qiime diversity alpha" + version="2020.8"> + <description>Alpha diversity</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ qiime diversity alpha --i-table=$itable + --p-metric=$pmetric --o-alpha-diversity=oalphadiversity + +#if str($examples) != 'None': +--examples=$examples +#end if + ; 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[ + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] 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="strong">strong</option> + <option value="observed_features">observed_features</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="gini_index">gini_index</option> + <option value="simpson_e">simpson_e</option> + <option value="osd">osd</option> + <option value="pielou_e">pielou_e</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="shannon">shannon</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="robbins">robbins</option> + <option value="doubles">doubles</option> + <option value="chao1">chao1</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> + </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}: 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] +table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence] 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') +metric : Str % Choices('mcintosh_e', 'esty_ci', 'chao1', 'observed_features', 'ace', 'margalef', 'berger_parker_d', 'simpson_e', 'doubles', 'gini_index', 'heip_e', 'michaelis_menten_fit', 'enspie', 'menhinick', 'shannon', 'pielou_e', 'singles', 'simpson', 'chao1_ci', 'strong', 'fisher_alpha', 'osd', 'dominance', 'robbins', 'lladser_pe', 'kempton_taylor_q', 'mcintosh_d', 'brillouin_d', 'goods_coverage') The alpha diversity metric to be computed. Returns ------- alpha_diversity : SampleData[AlphaDiversity] Vector containing per-sample alpha diversities. - ]]></help> -<macros> + ]]></help> + <macros> <import>qiime_citation.xml</import> -</macros> -<expand macro="qiime_citation"/> -</tool> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file