diff mothur/tools/mothur/get.otus.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/get.otus.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/get.otus.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_get_otus" name="Get.otus" version="1.16.0">
+<tool id="mothur_get_otus" name="Get.otus" version="1.19.0">
  <description>Get otus containing sequences from specified groups</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -9,15 +9,18 @@
   --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
+  #if $groupnames.source == 'groups':
+   #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0:
+    --groups=$groupnames.groups
+   #end if
+  #else
+   #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0:
+    --accnos=$groupnames.accnos
+   #end if
   #end if
   #set results = ["'^mothur.\S+\.logfile$:'" + $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__]
+  #set results = $results + ["'" + $re.sub(r'^(.*)\.(.*?)',r'\1.pick.' + $label.__str__ + r'.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__]
+  #set results = $results + ["'" + $re.sub(r'^(.*)\.(.*?)',r'\1.pick.'+ $label.__str__ + r'.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
   --result=#echo ','.join($results)
  </command>
  <inputs>
@@ -29,14 +32,25 @@
     <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"/>
+  <conditional name="groupnames">
+   <param name="source" type="select" label="Select Group Names from">
+    <option value="groups">A List of Group Names</option>
+    <option value="accnos">A History Group Name Accnos Dataset</option>
+   </param>
+   <when value="groups">
+    <param name="groups" type="select" label="groups - Pick groups to include" multiple="true"  force_select="true">
+     <help>At least one group must be selected</help>
+     <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>
+   </when>
+   <when value="accnos">
+    <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/>
+   </when>
+  </conditional>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -59,8 +73,9 @@
 
 **Command Documenation**
 
-The get.otus_ command selects otus containing sequences from a specific group or set of groups.
+The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups.
 
+.. _list: http://www.mothur.org/wiki/List_file
 .. _get.otus: http://www.mothur.org/wiki/Get.otus