diff mothur/tools/mothur/remove.groups.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/remove.groups.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/remove.groups.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,5 +1,5 @@
-<tool id="mothur_remove_groups" name="Remove.groups" version="1.16.0">
- <description>Remove groups</description>
+<tool id="mothur_remove_groups" name="Remove.groups" version="1.19.0">
+ <description>Remove groups from groups,fasta,names,list,taxonomy</description>
  <command interpreter="python">
   mothur_wrapper.py 
   #import re, os.path
@@ -9,11 +9,14 @@
   --cmd='remove.groups'
   --outputdir='$logfile.extra_files_path'
   --group=$group_in
-  #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
   #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0:
    --fasta=$fasta_in
@@ -36,24 +39,34 @@
  </command>
  <inputs>
   <param name="group_in" type="data" format="groups" label="group - Groups"/>
-  <param name="groups" type="select" optional="true" label="groups - Pick groups to remove" 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 - Accession Names"/>
-  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
+  <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 remove" 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>
+   </when>
+   <when value="accnos">
+    <param name="accnos" type="data" format="accnos" label="accnos - Group Names from your history"/>
+   </when>
+  </conditional>
+  <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/>
   <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
   <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
-  <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy"/>
+  <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
   <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/>
   <!-- fix format -->
-  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
+  <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
    <filter>fasta_in != None</filter>
   </data>
   <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name">
@@ -62,7 +75,7 @@
   <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
    <filter>list_in != None</filter>
   </data>
-  <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
+  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
    <filter>taxonomy_in != None</filter>
   </data>
  </outputs>
@@ -82,8 +95,12 @@
 
 **Command Documenation**
 
-The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy.
+The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_.
 
+.. _name: http://www.mothur.org/wiki/Name_file
+.. _group: http://www.mothur.org/wiki/Group_file
+.. _list: http://www.mothur.org/wiki/List_file
+.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
 .. _remove.groups: http://www.mothur.org/wiki/Remove.groups