diff qiime2/qiime_diversity-lib_weighted-unifrac.xml @ 14:a0a8d77a991c draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_diversity-lib_weighted-unifrac.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -0,0 +1,86 @@
+<?xml version="1.0" ?>
+<tool id="qiime_diversity-lib_weighted-unifrac" name="qiime diversity-lib weighted-unifrac"
+      version="2020.8">
+  <description>Weighted Unifrac</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime diversity-lib weighted-unifrac
+
+--i-table=$itable
+
+--i-phylogeny=$iphylogeny
+
+#if str($pthreads) != 'None':
+--p-threads=$pthreads
+#end if
+
+#if $pbypasstips:
+ --p-bypass-tips
+#end if
+
+--o-distance-matrix=odistancematrix
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp odistancematrix.qza $odistancematrix
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency] The feature table containing the samples for which Weighted Unifrac should be computed.      [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-phylogeny: ARTIFACT  Phylogenetic tree containing tip identifiers that Phylogeny[Rooted]     correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.                  [required]" name="iphylogeny" optional="False" type="data" />
+    <param label="--p-threads: " name="pthreads" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Int % Range(1">Int % Range(1</option>
+      <option value="None">None</option>
+    </param>
+    <param label="--p-bypass-tips: --p-bypass-tips: / --p-no-bypass-tips In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs                                [default: False]" name="pbypasstips" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Weighted Unifrac
+###############################################################
+
+Compute Weighted Unifrac for each sample in a feature table
+
+Parameters
+----------
+table : FeatureTable[Frequency | RelativeFrequency]
+    The feature table containing the samples for which Weighted Unifrac
+    should be computed.
+phylogeny : Phylogeny[Rooted]
+    Phylogenetic tree containing tip identifiers that 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.
+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.
+bypass_tips : Bool, optional
+    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
+
+Returns
+-------
+distance_matrix : DistanceMatrix
+    Distance matrix for Unweighted Unifrac.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file