--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align_seqs.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,127 @@
+<tool id="align_seqs" name="align_seqs" version="1.2.0">
+ <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=$align.alignment_method
+  #if $align.alignment_method == 'pynast':
+    --template_fp=$align.alignment.template_fp
+    --pairwise_alignment_method=$align.pairwise_alignment_method
+    --min_length=$align.min_length
+    --min_percent_id=$align.min_percent_id
+    --blast_db=$align.blast_db
+  #elif $align.alignment_method == 'infernal':
+    --template_fp=$align.alignment.template_fp
+  #elif $align.alignment_method == 'clustalw':
+    #echo ''
+  #elif $align.alignment_method == 'muscle':
+    #echo ''
+  #elif $align.alignment_method == 'mafft':
+    #echo ''
+  #end if
+
+  --output_dir='$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 [REQUIRED]"/>
+
+  <conditional name="align">
+    <param name="alignment_method" type="select" label="alignment_method"
+     help="Method for aligning sequences. Valid choices are: pynast, infernal, clustalw, muscle, infernal, mafft [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>
+  
+    <when value="pynast">
+      <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 from_file="mothur_aligndb.loc">
+          <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"
+         help="Filepath for template against [REQUIRED if for alignment_method  pynast or infernal]"/>
+       </when>
+      </conditional>
+      <param name="pairwise_alignment_method" type="select" label="pairwise_alignment_method"
+       help="method for performing pairwise alignment in PyNAST. Valid choices are muscle, pair_hmm, clustal, blast, uclust, mafft [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" 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" 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="text"  label="blast_db" optional="true"
+       help="Database to blast against when -m pynast [default: created on-the-fly from template_alignment]"/>
+    </when> <!-- pynast -->
+  
+    <when value="infernal">
+       <!-- Template alignment must be in Stockholm format with corresponding secondary structure annotation when using InfernalAligner. -->
+      <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 from_file="mothur_aligndb.loc">
+          <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"
+         help="Filepath for template against [REQUIRED if for alignment_method  pynast or infernal]"/>
+       </when>
+      </conditional>
+    </when> <!-- infernal -->
+
+    <when value="clustalw">
+    </when> <!-- clustalw -->
+    <when value="muscle">
+    </when> <!-- muscle -->
+    <when value="mafft">
+    </when> <!-- mafft -->
+  
+  </conditional> <!-- align -->
+
+
+ </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" >
+    <filter>align['alignment_method'] == 'pynast'</filter>
+   </data>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+