diff mothur/tools/mothur/otu.hierarchy.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/otu.hierarchy.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -0,0 +1,61 @@
+<tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.19.0">
+ <description>Relate OTUs at different distances</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  ## output {group_file_name}.pick.{label}.groups   {list_file_name}.pick.{label}.list 
+  #import re, os.path
+  --cmd='otu.hierarchy'
+  --outputdir='$logfile.extra_files_path'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.otu\.hierarchy$:'$hierarchy
+  --list=$list
+  --label=$label1,$label2
+  --output=$output
+ </command>
+ <inputs>
+  <param name="list" type="data" format="list" label="list - OTU List"/>
+  <param name="label1" type="select" label="label - OTU Label 1" >
+   <options from_dataset="list">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+   </options>
+  </param>
+  <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1">
+   <options from_dataset="list">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+    <filter type="param_value" ref="label1" column="value" keep="false"/>
+   </options>
+  </param>
+  <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers">
+   <option value="name" selected="treu">OTU sequence names</option>
+   <option value="number">OTU numbers</option>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/>
+ </outputs>
+ <requirements>
+  <requirement type="binary">mothur</requirement>
+ </requirements>
+ <tests>
+ </tests>
+ <help>
+**Mothur Overview**
+
+Mothur_, initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan,
+provides bioinformatics for the microbial ecology community.
+
+.. _Mothur: http://www.mothur.org/wiki/Main_Page
+
+**Command Documenation**
+
+The otu.hierarchy_ command relates OTUs from a list_ at different distances.
+
+.. _list_file: http://www.mothur.org/wiki/List_file
+.. _otu.hierarchy: http://www.mothur.org/wiki/Otu.hierarchy
+
+
+ </help>
+</tool>