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diff qiime2/qiime_diversity_beta-phylogenetic.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-phylogenetic.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_diversity_beta-phylogenetic.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,64 +1,80 @@
 <?xml version="1.0" ?>
-<tool id="qiime_diversity_beta-phylogenetic" name="qiime diversity beta-phylogenetic" version="2019.7">
-	<description> - Beta diversity (phylogenetic)</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_diversity_beta-phylogenetic" name="qiime diversity beta-phylogenetic"
+      version="2020.8">
+  <description>Beta diversity (phylogenetic)</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime diversity beta-phylogenetic
 
 --i-table=$itable
+
 --i-phylogeny=$iphylogeny
+
 --p-metric=$pmetric
 
-#set $pnjobs = '${GALAXY_SLOTS:-4}'
-#if str($pnjobs):
- --p-n-jobs="$pnjobs"
+#if str($pthreads) != 'None':
+--p-threads=$pthreads
 #end if
 
-
 #if $pvarianceadjusted:
  --p-variance-adjusted
 #end if
 
 #if str($palpha):
- --p-alpha="$palpha"
+  --p-alpha=$palpha
 #end if
-
 #if $pbypasstips:
  --p-bypass-tips
 #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 format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data"/>
-		<param label="--p-metric: " name="pmetric" optional="False" type="select">
-			<option value="generalized_unifrac">generalized_unifrac</option>
-			<option value="unweighted_unifrac">unweighted_unifrac</option>
-			<option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
-			<option value="weighted_unifrac">weighted_unifrac</option>
-		</param>
-		<param label="--p-variance-adjusted: --p-no-variance-adjusted Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.                         [default: False]" name="pvarianceadjusted" selected="False" type="boolean"/>
-		<param label="--p-alpha: PROPORTION Range(0, 1, inclusive_end=True) This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.             [optional]" name="palpha" optional="True" min="0" max="1" exclude_max="False"  type="float"/>
-		<param label="--p-bypass-tips: --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs                                [default: False]" name="pbypasstips" selected="False" type="boolean"/>
-	</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 format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data" />
+    <param label="--p-metric: " name="pmetric" optional="False" type="select">
+      <option value="weighted_unifrac">weighted_unifrac</option>
+      <option value="unweighted_unifrac">unweighted_unifrac</option>
+      <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
+      <option value="generalized_unifrac">generalized_unifrac</option>
+    </param>
+    <param label="--p-threads: " name="pthreads" 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="--p-variance-adjusted: --p-variance-adjusted: / --p-no-variance-adjusted Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation.                         [default: False]" name="pvarianceadjusted" selected="False" type="boolean" />
+    <param label="--p-alpha: PROPORTION Range(0, 1, inclusive_end=True) This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized.             [optional]" name="palpha" optional="False" type="text" />
+    <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs                                [default: False]" name="pbypasstips" selected="False" type="boolean" />
+    <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 (phylogenetic)
-#############################
+###############################################################
 
 Computes a user-specified phylogenetic 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.
 phylogeny : Phylogeny[Rooted]
@@ -66,8 +82,12 @@
     feature identifiers in the table. This tree can contain tip ids that
     are not present in the table, but all feature ids in the table must be
     present in this tree.
-metric : Str % Choices('weighted_unifrac', 'generalized_unifrac', 'weighted_normalized_unifrac', 'unweighted_unifrac')
+metric : Str % Choices('generalized_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac', 'unweighted_unifrac')
     The beta diversity metric to be computed.
+threads : Int % Range(1, None) | Str % Choices('auto'), optional
+    The number of CPU threads to use in performing this calculation. May
+    not exceed the number of available physical cores. If threads = 'auto',
+    one thread will be created for each identified CPU core on the host.
 variance_adjusted : Bool, optional
     Perform variance adjustment based on Chang et al. BMC Bioinformatics
     2011. Weights distances based on the proportion of the relative
@@ -87,11 +107,11 @@
 
 Returns
 -------
-distance_matrix : DistanceMatrix % Properties('phylogenetic')
+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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