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

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

--- a/mothur/tools/mothur/remove.seqs.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/remove.seqs.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_remove_seqs" name="Remove.seqs" version="1.16.0">
+<tool id="mothur_remove_seqs" name="Remove.seqs" version="1.19.0">
  <description>Remove sequences by name</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -47,7 +47,7 @@
   <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/>
   <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/>
   <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"/>
   <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/>
  </inputs>
  <outputs>
@@ -83,7 +83,7 @@
   <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>
@@ -103,8 +103,14 @@
 
 **Command Documenation**
 
-The remove.seqs_ command takes a list of sequence names and either a fasta, name, group, list, or align.report file to generate a new file that does not contain the sequences in the list. This command may be used in conjunction with the list.seqs command to help screen a sequence collection.
+The remove.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that does not contain the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.
 
+.. _name: http://www.mothur.org/wiki/Name_file
+.. _group: http://www.mothur.org/wiki/Group_file
+.. _list: http://www.mothur.org/wiki/List_file
+.. _align.report: http://www.mothur.org/wiki/Align.seqs
+.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
+.. _list.seqs: http://www.mothur.org/wiki/list.seqs
 .. _remove.seqs: http://www.mothur.org/wiki/Remove.seqs
 
  </help>