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

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

--- a/mothur/tools/mothur/remove.lineage.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/remove.lineage.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_remove_lineage" name="Remove.lineage" version="1.16.0">
+<tool id="mothur_remove_lineage" name="Remove.lineage" version="1.19.0">
  <description>Picks by taxon</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -20,7 +20,7 @@
   #end if
   #if $alignreport_in.__str__ != "None" and len($alignreport_in.__str__) > 0:
    --alignreport=$alignreport_in
-   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__]
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.pick.align.report',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__]
   #end if
   #if $list_in.__str__ != "None" and len($list_in.__str__) > 0:
    --list=$list_in
@@ -34,7 +34,7 @@
   --result=#echo ','.join($results)
  </command>
  <inputs>
-  <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy"/>
+  <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/>
   <param name="taxons" type="select" size="120" label="Browse Taxons from Taxonomy">
    <options from_dataset="taxonomy">
     <column name="name" index="1"/>
@@ -53,7 +53,7 @@
  <outputs>
   <!-- fix format -->
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/>
+  <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/>
   <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
    <filter>fasta_in != None</filter>
   </data>
@@ -86,8 +86,13 @@
 
 **Command Documenation**
 
-The remove.lineage_ command reads a taxonomy file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name, group, list, or align.report file to this command and mothur will generate new files for each of those containing only the selected sequences.
+The remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta_, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences.
 
+.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
+.. _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
 .. _remove.lineage: http://www.mothur.org/wiki/Remove.lineage