diff qiime2/qiime_diversity_alpha.xml @ 14:a0a8d77a991c draft

Uploaded

--- 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>
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