diff mothur/tools/mothur/get.otus.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 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.otus.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,68 @@
+<tool id="mothur_get_otus" name="Get.otus" version="1.15.0">
+ <description>Get otus containing sequences from specified groups</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.otus'
+  --outputdir='$logfile.extra_files_path'
+  --group=$group_in
+  --list=$list_in
+  --label=$label
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+   --groups=$groups
+  #end if
+  #if $accnos.__str__ != "None" and len($accnos.__str__) > 0:
+   --accnos=$accnos
+  #end if
+  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.' + $label.__str__ + '.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__]
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.'+ $label.__str__ + '.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
+  --result=#echo ','.join($results)
+ </command>
+ <inputs>
+  <param name="group_in" type="data" format="groups" label="group - Groups"/>
+  <param name="list_in" type="data" format="list" label="list - OTU List"/>
+  <param name="label" type="select" label="label - OTU Labels" >
+   <options from_dataset="list_in">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+   </options>
+  </param>
+  <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
+   <options from_dataset="group_in">
+    <column name="name" index="1"/>
+    <column name="value" index="1"/>
+    <filter type="unique_value" name="unq_grp" column="1" />
+   </options>
+  </param>
+  <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/>
+  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/>
+ </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.otus_ command selects otus containing sequences from a specific group or set of groups.
+
+.. _get.otus: http://www.mothur.org/wiki/Get.otus
+
+
+ </help>
+</tool>