diff mothur/tools/mothur/sub.sample.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/sub.sample.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/sub.sample.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_sub_sample" name="Sub.sample" version="1.16.0">
+<tool id="mothur_sub_sample" name="Sub.sample" version="1.19.0">
  <description>Create a sub sample</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -12,26 +12,30 @@
    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.fasta_in.__str__)) + ":'" + $fasta_out.__str__]
    #if $input.name_in.__str__ != "None" and len($input.name_in.__str__) > 0:
     --name=$input.name_in
-    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.name_in.__str__)) + ":'" + $names_out.__str__]
+    ## #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.name_in.__str__)) + ":'" + $names_out.__str__]
    #end if
-   #if $input.use_group.group_in.__str__ != "None" and len($input.use_group.group_in.__str__) > 0:
-    --group=$input.use_group.group_in
-    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.use_group.group_in.__str__)) + ":'" + $group_out.__str__]
-    #if $input.use_group.groups.__str__ != "None" and len($input.use_group.groups.__str__) > 0:
-     --groups=$input.use_group.groups
+   #if $input.use_group.to_filter == "yes":
+    #if $input.use_group.group_in.__str__ != "None" and len($input.use_group.group_in.__str__) > 0:
+     --group=$input.use_group.group_in
+     #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.use_group.group_in.__str__)) + ":'" + $group_out.__str__]
+     #if $input.use_group.groups.__str__ != "None" and len($input.use_group.groups.__str__) > 0:
+      --groups=$input.use_group.groups
+     #end if
+     $input.use_group.persample
     #end if
-    $input.use_group.persample
    #end if
   #elif $input.format == "list":
    --list=$input.otu_in
    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $list_out.__str__]
-   #if $input.use_group.group_in.__str__ != "None" and len($input.use_group.group_in.__str__) > 0:
-    --group=$input.use_group.group_in
-    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.use_group.group_in.__str__)) + ":'" + $group_out.__str__]
-    #if $input.use_group.groups.__str__ != "None" and len($input.use_group.groups.__str__) > 0:
-     --groups=$input.use_group.groups
+   #if $input.use_group.to_filter == "yes":
+    #if $input.use_group.group_in.__str__ != "None" and len($input.use_group.group_in.__str__) > 0:
+     --group=$input.use_group.group_in
+     #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.use_group.group_in.__str__)) + ":'" + $group_out.__str__]
+     #if $input.use_group.groups.__str__ != "None" and len($input.use_group.groups.__str__) > 0:
+      --groups=$input.use_group.groups
+     #end if
+     $input.use_group.persample
     #end if
-    $input.use_group.persample
    #end if
    #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
     --label=$input.label
@@ -176,9 +180,11 @@
   <data format="rabund" name="rabund_out" label="${tool.name} on ${on_string}: subsample.rabund">
    <filter>input['format'] == 'rabund'</filter>
   </data>
+  <!--  This doesn't appear to be generated even though the documentation says it is
   <data format="names" name="names_out" label="${tool.name} on ${on_string}: subsample.names">
    <filter>(input['format'] == 'fasta' and input['name_in'] != None)</filter>
   </data>
+  -->
   <data format="groups" name="group_out" label="${tool.name} on ${on_string}: subsample.groups">
    <filter>input['use_group']['group_in'] != None</filter>
   </data>
@@ -199,8 +205,12 @@
 
 **Command Documenation**
 
-The sub.sample_ command selects otus containing sequences from a specific group or set of groups.
+The sub.sample_ command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list_, shared_, rabund_ and sabund_ to generate a new file that contains a sampling of your original file.
 
+.. _list: http://www.mothur.org/wiki/List_file
+.. _shared: http://www.mothur.org/wiki/Shared_file
+.. _rabund: http://www.mothur.org/wiki/Rabund_file
+.. _sabund: http://www.mothur.org/wiki/Sabund_file
 .. _sub.sample: http://www.mothur.org/wiki/Sub.sample