diff qiime2-2020.8/qiime_phylogeny_robinson-foulds.xml @ 20:d93d8888f0b0 draft

Uploaded

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+++ b/qiime2-2020.8/qiime_phylogeny_robinson-foulds.xml	Fri Sep 04 12:44:24 2020 +0000
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+<?xml version="1.0" ?>
+<tool id="qiime_phylogeny_robinson-foulds" name="qiime phylogeny robinson-foulds"
+      version="2020.8">
+  <description>Calculate Robinson-Foulds distance between phylogenetic trees.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime phylogeny robinson-foulds
+
+--i-trees=$itrees
+
+#if str($plabels):
+  --p-labels=$plabels
+#end if
+#if str($pmissingtips) != 'None':
+--p-missing-tips=$pmissingtips
+#end if
+
+--o-distance-matrix=odistancematrix
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp odistancematrix.qza $odistancematrix
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-trees: ARTIFACTS... List[Phylogeny[Rooted | Unrooted]] Phylogenetic trees to compare with Robinson-Foulds. Rooting information and branch lengths are ignored by this metric.                           [required]" name="itrees" optional="False" type="data" />
+    <param label="--p-labels: TEXT...      Labels to use for the tree names in the distance List[Str]             matrix. If ommited, labels will be \'tree_n\' where \'n\' ranges from 1..N. The number of labels must match the number of trees.                [optional]" name="plabels" optional="False" type="text" />
+    <param label="--p-missing-tips: " name="pmissingtips" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="error">error</option>
+      <option value="intersect-all">intersect-all</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: distancematrix.qza" name="odistancematrix" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Calculate Robinson-Foulds distance between phylogenetic trees.
+###############################################################
+
+Calculate the Robinson-Foulds symmetric difference metric between two or
+more phylogenetic trees.
+
+Parameters
+----------
+trees : List[Phylogeny[Rooted | Unrooted]]
+    Phylogenetic trees to compare with Robinson-Foulds. Rooting information
+    and branch lengths are ignored by this metric.
+labels : List[Str], optional
+    Labels to use for the tree names in the distance matrix. If ommited,
+    labels will be "tree_n" where "n" ranges from 1..N. The number of
+    labels must match the number of trees.
+missing_tips : Str % Choices('error', 'intersect-all'), optional
+    How to handle tips that are not shared between trees. "error" will
+    raise an error if the set of tips is not identical between all input
+    trees. "intersect-all" will remove tips that are not shared between all
+    trees before computing distances beteen trees.
+
+Returns
+-------
+distance_matrix : DistanceMatrix
+    The distances between trees as a symmetric matrix.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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