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

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

--- a/mothur/tools/mothur/align.seqs.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/align.seqs.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,12 +1,12 @@
-<tool id="mothur_align_seqs" name="Align.seqs" version="1.16.0">
+<tool id="mothur_align_seqs" name="Align.seqs" version="1.19.0">
  <description>Align sequences to a template alignment</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='align.seqs'
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.align$:'$out_file,'^\S+\.align\.report$:'$report
   --outputdir='$logfile.extra_files_path'
-  --candidate=$candidate
-  --template=$alignment.template
+  --fasta=$candidate
+  --reference=$alignment.template
   #if $search.method == 'kmer': 
    --ksize=$search.ksize
   #else: 
@@ -26,22 +26,22 @@
   --processors=2
  </command>
  <inputs>
-  <param name="candidate" type="data" format="fasta" label="candidate - Candiate Sequences"/>
+  <param name="candidate" type="data" format="fasta" label="fasta - Candiate Sequences"/>
   <conditional name="alignment">
-   <param name="source" type="select" label="Select Template from" help="">
-    <option value="hist">History</option>
+   <param name="source" type="select" label="Select Reference Template from" help="">
     <option value="ref">Cached Reference</option>
+    <option value="history">Your History</option>
    </param>
    <when value="ref">
-    <param name="template" type="select" label="template - Select an alignment database " help="">
+    <param name="template" type="select" label="reference - Select an alignment database " help="">
      <options from_file="mothur_aligndb.loc">
       <column name="name" index="0" />
       <column name="value" index="1" />
      </options>
     </param>
    </when>
-   <when value="hist">
-    <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/>
+   <when value="history">
+    <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
    </when>
   </conditional>
   <conditional name="search">
@@ -111,8 +111,16 @@
 
 **Command Documenation**
 
-The align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template alignment.
+The align.seqs_ command aligns a user-supplied fasta-formatted candidate sequence file to a user-supplied fasta-formatted template_alignment_.
 
+The general approach is to
+ i) find the closest template for each candidate using kmer searching, blastn, or suffix tree searching;
+ ii) to make a pairwise alignment between the candidate and de-gapped template sequences using the Needleman-Wunsch, Gotoh, or blastn algorithms; and
+ iii) to re-insert gaps to the candidate and template pairwise alignments using the NAST algorithm so that the candidate sequence alignment is compatible with the original template alignment.
+
+In general the alignment is very fast - we are able to align over 186,000 full-length sequences to the SILVA alignment in less than 3 hrs with a quality as good as the SINA aligner. Furthermore, this rate can be accelerated using multiple processors. While the aligner doesn't explicitly take into account the secondary structure of the 16S rRNA gene, if the template database is based on the secondary structure, then the resulting alignment will at least be implicitly based on the secondary structure.
+
+.. _template_alignment: http://www.mothur.org/wiki/Alignment_database
 .. _align.seqs: http://www.mothur.org/wiki/Align.seqs