--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align_seqs.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,128 @@
+<tool id="qiime_align_seqs" name="Align sequences" version="1.9.1">
+    <description>using a variety of alignment methods</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <version_command><![CDATA[
+        align_seqs.py --version
+    ]]>
+    </version_command>
+
+    <command>
+<![CDATA[
+        align_seqs.py 
+            -i $input_fasta_fp
+            -o align_seqs
+            -m $alignment.alignment_method
+
+            #if $alignment.alignment_method == 'pynast':
+                -a $alignment.pairwise_alignment_method
+            #end if
+
+            #if str($template_fp) != 'None':
+                -t $template_fp
+            #end if
+
+            #if $min_length:
+                -e $min_length
+            #end if
+
+            -p $min_percent_id
+]]>
+    </command>
+
+    <inputs>
+        <param name="input_fasta_fp" type="data" format="fasta" 
+            label="Input fasta file" help="(-i/--input_fasta_fp)"/> 
+
+        <conditional name="alignment">
+            <param name="alignment_method" type="select" 
+                label="Method for aligning sequences" help="(-m/--alignment_method)">
+                <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">
+                <param name="pairwise_alignment_method" type="select" 
+                    label="Method for performing pairwise alignment in PyNAST" 
+                    help="(-a/--pairwise_alignment_method)">
+                    <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>
+            </when>
+            <when value="infernal" />
+            <when value="clustalw" />
+            <when value="muscle" />
+            <when value="mafft" />
+        </conditional>
+
+        <param name="template_fp" type="data" format="fasta" 
+            label="Fasta file for template alignment" help="(-t/--template_fp)" 
+            optional="True"/> 
+
+        <param name="min_length" type="integer" label="Minimum sequence 
+            length to include in alignment" help="By default, 75% of the median 
+            input sequence length (-e/--min_length)" optional="True"/>
+
+        <param name="min_percent_id" type="float" value="0.75" label="Minimum 
+            percent sequence identity to closest blast hit to include sequence 
+            in alignment" help="(-p/--min_percent_id)"/>
+    </inputs>
+
+    <outputs>
+        <data name="aligned_sequences" format="fasta" 
+            from_work_dir="align_seqs/*_aligned.fasta" 
+            label="${tool.name} on ${on_string}: Aligned sequences" />
+
+        <data name="failures_sequences" format="fasta" 
+            from_work_dir="align_seqs/*_failures.fasta" 
+            label="${tool.name} on ${on_string}: Failure sequences">
+            <filter> alignment['alignment_method'] == 'pynast'</filter>
+        </data>
+
+        <data name="log" format="txt" from_work_dir="align_seqs/*_log.txt" 
+            label="${tool.name} on ${on_string}: Log"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_fasta_fp" value=""/> 
+            <param name="alignment_method" value="pynast"/>
+            <param name="pairwise_alignment_method" value="muscle"/>
+            <param name="min_percent_id" value="0.75" />
+            <output name="aligned_sequences" 
+                value="align_seqs_aligned_sequences.fasta"/>
+            <output name="failures_sequences" 
+                value="align_seqs_failures_sequences.fasta"/>
+            <output name="log" value="align_seqs_log.txt"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does?**
+
+This tool aligns the sequences in a FASTA file to each other or to a template sequence alignment, depending on the method chosen. 
+
+More information about this tool is available on 
+`QIIME documentation <http://qiime.org/scripts/align_seqs.html>`_.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+        <citation type="doi">10.1093/bioinformatics/btp636</citation>
+        <citation type="doi">10.1093/nar/gkh340</citation>
+        <citation type="doi">10.1093/bioinformatics/btp157</citation>
+    </citations>
+</tool>