diff qiime2/qiime_gneiss_assign-ids.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_gneiss_assign-ids.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_gneiss_assign-ids.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,32 +1,46 @@
 <?xml version="1.0" ?>
-<tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids" version="2019.7">
-	<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="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_gneiss_assign-ids" name="qiime gneiss assign-ids"
+      version="2020.8">
+  <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="2020.8">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
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-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 ${on_string}: outputtree.qza" name="ooutputtree"/>
-	</outputs>
-	<help><![CDATA[
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-input-table: ARTIFACT FeatureTable[Frequency] The input table of counts.                   [required]" name="iinputtable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-input-tree: ARTIFACT Phylogeny[Rooted]  The input tree with potential missing ids.   [required]" name="iinputtree" optional="False" type="data" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: outputtable.qza" name="ooutputtable" />
+    <data format="qza" label="${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
@@ -45,9 +59,9 @@
     A table with features matching the tree tips.
 output_tree : Hierarchy
     A tree with uniquely identifying ids.
-	]]></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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