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diff qiime2/qiime_diversity_beta.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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--- a/qiime2/qiime_diversity_beta.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_diversity_beta.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,86 +1,105 @@
 <?xml version="1.0" ?>
-<tool id="qiime_diversity_beta" name="qiime diversity beta" version="2019.7">
-	<description> - Beta diversity</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_diversity_beta" name="qiime diversity beta"
+      version="2020.8">
+  <description>Beta diversity</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime diversity beta
 
 --i-table=$itable
 
 --p-metric=$pmetric
 
-#if str($ppseudocount):
- --p-pseudocount=$ppseudocount
-#end if
+--p-pseudocount=$ppseudocount
 
-#set $pnjobs = '${GALAXY_SLOTS:-4}'
-#if str($pnjobs):
- --p-n-jobs="$pnjobs"
+#if str($pnjobs) != 'None':
+--p-n-jobs=$pnjobs
 #end if
 
 --o-distance-matrix=odistancematrix
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
 cp odistancematrix.qza $odistancematrix
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table containing the samples over which beta diversity should be computed.           [required]" name="itable" optional="False" type="data"/>
-		<param label="--p-metric: " name="pmetric" optional="False" type="select">
-			<option value="kulsinski">kulsinski</option>
-			<option value="wminkowski">wminkowski</option>
-			<option value="correlation">correlation</option>
-			<option value="hamming">hamming</option>
-			<option value="canberra">canberra</option>
-			<option value="canberra_adkins">canberra_adkins</option>
-			<option value="sqeuclidean">sqeuclidean</option>
-			<option value="sokalmichener">sokalmichener</option>
-			<option value="cityblock">cityblock</option>
-			<option value="braycurtis">braycurtis</option>
-			<option value="matching">matching</option>
-			<option value="russellrao">russellrao</option>
-			<option value="cosine">cosine</option>
-			<option value="yule">yule</option>
-			<option value="euclidean">euclidean</option>
-			<option value="rogerstanimoto">rogerstanimoto</option>
-			<option value="seuclidean">seuclidean</option>
-			<option value="jaccard">jaccard</option>
-			<option value="sokalsneath">sokalsneath</option>
-			<option value="aitchison">aitchison</option>
-			<option value="chebyshev">chebyshev</option>
-			<option value="dice">dice</option>
-			<option value="mahalanobis">mahalanobis</option>
-		</param>
-		<param label="--p-pseudocount: INTEGER Range(1, None)     A pseudocount to handle zeros for compositional metrics.  This is ignored for other metrics. [default: 1]" name="ppseudocount" optional="True" type="integer" min="1" value="1"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix"/>
-	</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 over which beta diversity should be computed.           [required]" name="itable" optional="False" type="data" />
+    <param label="--p-metric: " name="pmetric" optional="False" type="select">
+      <option value="braycurtis">braycurtis</option>
+      <option value="euclidean">euclidean</option>
+      <option value="cityblock">cityblock</option>
+      <option value="cosine">cosine</option>
+      <option value="minkowski">minkowski</option>
+      <option value="matching">matching</option>
+      <option value="correlation">correlation</option>
+      <option value="russellrao">russellrao</option>
+      <option value="sokalsneath">sokalsneath</option>
+      <option value="seuclidean">seuclidean</option>
+      <option value="canberra">canberra</option>
+      <option value="sokalmichener">sokalmichener</option>
+      <option value="kulsinski">kulsinski</option>
+      <option value="jensenshannon">jensenshannon</option>
+      <option value="jaccard">jaccard</option>
+      <option value="hamming">hamming</option>
+      <option value="chebyshev">chebyshev</option>
+      <option value="yule">yule</option>
+      <option value="dice">dice</option>
+      <option value="sqeuclidean">sqeuclidean</option>
+      <option value="aitchison">aitchison</option>
+      <option value="canberra_adkins">canberra_adkins</option>
+      <option value="rogerstanimoto">rogerstanimoto</option>
+    </param>
+    <param label="--p-pseudocount: INTEGER Range(1, None)     A pseudocount to handle zeros for compositional metrics.  This is ignored for other metrics. [default: 1]" min="1" name="ppseudocount" optional="True" type="integer" value="1" />
+    <param label="--p-n-jobs: " name="pnjobs" 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}: distancematrix.qza" name="odistancematrix" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Beta diversity
-##############
+###############################################################
 
 Computes a user-specified beta diversity metric for all pairs of samples in
 a feature table.
 
 Parameters
 ----------
-table : FeatureTable[Frequency]
+table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]
     The feature table containing the samples over which beta diversity
     should be computed.
-metric : Str % Choices('sokalmichener', 'yule', 'russellrao', 'rogerstanimoto', 'aitchison', 'correlation', 'jaccard', 'cosine', 'euclidean', 'sqeuclidean', 'chebyshev', 'cityblock', 'matching', 'dice', 'mahalanobis', 'wminkowski', 'kulsinski', 'seuclidean', 'sokalsneath', 'canberra', 'canberra_adkins', 'hamming', 'braycurtis')
+metric : Str % Choices('yule', 'cityblock', 'matching', 'russellrao', 'seuclidean', 'jaccard', 'braycurtis', 'minkowski', 'sokalmichener', 'aitchison', 'canberra_adkins', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'sokalsneath', 'correlation', 'hamming', 'dice', 'rogerstanimoto', 'canberra', 'chebyshev', 'jensenshannon')
     The beta diversity metric to be computed.
 pseudocount : Int % Range(1, None), optional
     A pseudocount to handle zeros for compositional metrics.  This is
     ignored for other metrics.
+n_jobs : Int % Range(1, None) | Str % Choices('auto'), optional
+    The number of concurrent jobs to use in performing this calculation.
+    May not exceed the number of available physical cores. If n_jobs =
+    'auto', one job will be launched for each identified CPU core on the
+    host.
 
 Returns
 -------
 distance_matrix : DistanceMatrix
     The resulting distance matrix.
-	]]></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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