diff qiime2/qiime_gneiss_assign-ids.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_gneiss_assign-ids.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,53 @@
+<?xml version="1.0" ?>
+<tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.4">
+	<description> - Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime gneiss assign-ids
+
+--i-input-table=$iinputtable
+--i-input-tree=$iinputtree
+
+--o-output-table=ooutputtable
+--o-output-tree=ooutputtree
+;
+cp ooutputtable.qza $ooutputtable;
+cp ooutputtree.qza $ooutputtree
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts.                   [required]" name="iinputtable" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted]  The input tree with potential missing ids.   [required]" name="iinputtree" optional="False" type="data"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable"/>
+		<data format="qza" label="${tool.name} on ${on_string}: outputtree.qza" name="ooutputtree"/>
+	</outputs>
+	<help><![CDATA[
+Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.
+##########################################################################################################
+
+Assigns UUIDs to uniquely identify internal nodes in the tree.  Also
+corrects for polytomies to create strictly bifurcating trees and aligns the
+table columns with the tree tip names
+
+Parameters
+----------
+input_table : FeatureTable[Frequency]
+    The input table of counts.
+input_tree : Phylogeny[Rooted]
+    The input tree with potential missing ids.
+
+Returns
+-------
+output_table : FeatureTable[Frequency]
+    A table with features matching the tree tips.
+output_tree : Hierarchy
+    A tree with uniquely identifying ids.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>