--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/align_seqs.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,93 @@
+<tool id="align_seqs" name="align_seqs" version="2.0.0">
+ <description>Align sequences using a variety of alignment methods</description>
+ <requirements>
+  <requirement type="binary">align_seqs.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_outputdir='$log.extra_files_path'
+  --galaxy_datasets='^\S+_aligned\.\S+$:'$aligned_fasta,'^\S+_log\.txt$:'$log,'^\S+_failures\.fasta$:'$failures
+  align_seqs.py
+  --input_fasta_fp=$input_fasta_fp
+  --alignment_method=$alignment_method
+  #if $alignment_method.__str__ == 'pynast':
+    #if $alignment.template_fp != None and $alignment.template_fp.__str__ != 'None' and $alignment.template_fp.__str__ != '':
+    --template_fp=$alignment.template_fp
+    #end if
+    --pairwise_alignment_method=$pairwise_alignment_method
+    --min_length=$min_length
+    --min_percent_id=$min_percent_id
+    #if $blast_db != None and $blast_db.__str__ != 'None' and $blast_db.__str__ != '':
+    --blast_db=$blast_db
+    #end if
+  #elif $alignment_method.__str__ == 'infernal':
+    --template_fp=$alignment.template_fp
+  #end if
+
+  --output_dir='$log.extra_files_path'
+ </command>
+ <inputs>
+  <param name="input_fasta_fp" type="data" format="fasta" label="input_fasta_fp" help="path to the input fasta file (usually output from pick_rep_set) [REQUIRED]"/>
+    <param name="alignment_method" type="select" label="alignment_method"
+     help="Method for aligning sequences. [default: pynast]">
+      <option value="pynast" selected="true">pynast</option>
+      <option value="infernal">infernal</option>
+      <option value="clustalw">clustalw</option>
+      <option value="muscle">muscle</option>
+      <option value="mafft">mafft</option>
+    </param>
+    <conditional name="alignment">
+       <param name="source" type="select" label="Select Template from" help="">
+        <option value="hist">History</option>
+        <option value="ref">Cached Reference</option>
+       </param>
+       <when value="ref">
+        <param name="template_fp" type="select" label="template - Select an alignment database " help="">
+         <options>
+          <column name="name" index="0" />
+          <column name="value" index="1" />
+         </options>
+        </param>
+       </when>
+       <when value="hist">
+        <param name="template_fp" type="data" format="txt" label="template_fp" optional="true"
+         help="Filepath for template against [REQUIRED ONLY if for alignment_method pynast or infernal]"/>
+       </when>
+      </conditional> <!--alignment-->
+      <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
+       help="Method for performing pairwise alignment; only required for PyNAST. [default: uclust]">
+        <option value="muscle">muscle</option>
+        <option value="pair_hmm">pair_hmm</option>
+        <option value="clustal">clustal</option>
+        <option value="blast">blast</option>
+        <option value="uclust" selected="true">uclust</option>
+        <option value="mafft">mafft</option>
+      </param>
+      <param name="min_length" type="integer" optional="true" value="150" label="min_length"
+       help="Minimum sequence length to include in alignment [default: 150]"/>
+      <param name="min_percent_id" type="float" value="0.75" optional="true" label="min_percent_id"
+       help="Minimum percent sequence identity to closest blast hit to include sequence in alignment [default: 0.75]"/>
+      <param name="blast_db" type="data" format="txt"  label="blast_db" optional="true"
+       help="Database to blast against when -m pynast [default: created on-the-fly from template_alignment]"/>
+      <!-- Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner. -->
+    
+ </inputs>
+ <outputs>
+   <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
+   <data format="fasta" name="aligned_fasta" label="${tool.name} on ${on_string}: aligned fasta" />
+   <data format="fasta" name="failures" label="${tool.name} on ${on_string}: failures" />
+ </outputs>
+ <tests>
+ </tests>
+ <help>  .. class:: warningmark
+Note: MUSCLE alignment is still not verified. Use at your own risk.
+  
+For more information, see align_seqs_ in the Qiime documentation.
+ 
+Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
+
+Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN  
+
+.. _align_seqs: http://qiime.org/scripts/align_seqs.html</help>
+</tool>
+