diff mothur/tools/mothur/get.otulist.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/get.otulist.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -0,0 +1,63 @@
+<tool id="mothur_get_otulist" name="Get.otulist" force_history_refresh="True" version="1.19.0">
+ <description>Get otus for each distance in a otu list</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='get.otulist'
+  --result='^mothur.\S+\.logfile$:'$logfile
+  --outputdir='$logfile.extra_files_path'
+  #if $as_datasets.__str__ == "yes":
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^\S+?\.((unique|[0-9.]*)\.otu)$:tabular'
+  #end if
+  --list=$list_in
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label=$label
+  #end if
+  #if $sort.__str__ != "None" and len($sort.__str__) > 0:
+   --sort=$sort
+  #end if
+ </command>
+ <inputs>
+  <param name="list_in" type="data" format="list" label="list - OTU List"/>
+  <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected.">
+   <options from_dataset="list_in">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+   </options>
+  </param>
+  <param name="sort" type="select" label="sort - select the output format">
+    <help>If otu is selected the output will be otu number followed by the list of names in that otu. 
+          If name is selected the output will be a sequence name followed by its otu number.</help>
+    <option value="otu" selected="true">otu</option>
+    <option value="name">name</option>
+  </param>
+  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label list"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+ </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 get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU.
+
+.. _get.otulist: http://www.mothur.org/wiki/Get.otulist
+
+
+ </help>
+</tool>