--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_alignment.xml	Tue Feb 02 05:50:37 2016 -0500
@@ -0,0 +1,102 @@
+<tool id="qiime_filter_alignment" name="filter alignment" version="1.9.1galaxy1">
+    <description>Filter sequence alignment by removing highly variable 
+        regions</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <command><![CDATA[
+        filter_alignment.py -i $input_fasta_file -o filter_alignment_output
+            #if str($lane_mask_fp) != 'None':
+             -m $lane_mask_fp
+            #end if
+
+            #if $suppress_lane_mask_filter:
+             -s
+            #end if
+
+            #if $allowed_gap_frac:
+             -g $allowed_gap_frac
+            #end if
+
+            #if $remove_outliers:
+             -r
+            #end if
+
+            #if $threshold:
+             -t $threshold
+            #end if
+
+            #if $entropy_threshold:
+             -e $entropy_threshold
+            #end if
+ ]]>
+    </command>
+
+    <inputs>
+        <param label="-i/--input_fasta_file: the input fasta file containing the 
+            alignment" name="input_fasta_file" optional="False" type="data"/>
+        <param default="None" label="-m/--lane_mask_fp: path to lane mask file 
+            [default: 16S alignment lane mask (Lane, D.J. 1991)]" 
+            name="lane_mask_fp" optional="True" type="data"/>
+        <param label="-s/--suppress_lane_mask_filter: suppress lane mask filtering 
+            [default: False]" name="suppress_lane_mask_filter" selected="False" 
+            type="boolean"/>
+        <param default="0.999999" label="-g/--allowed_gap_frac: gap filter threshold, 
+            filters positions which are gaps in &gt; allowed_gap_frac of the 
+            sequences [default: 0.999999]" name="allowed_gap_frac" optional="True" 
+            type="float"/>
+        <param label="-r/--remove_outliers: remove seqs very dissimilar to the 
+            alignment consensus (see --threshold).  [default: False]" 
+            name="remove_outliers" selected="False" type="boolean"/>
+        <param default="3.0" label="-t/--threshold: with -r, remove seqs whose 
+            dissimilarity to the consensus sequence is approximately &gt; x standard 
+            deviations above the mean of the sequences [default: 3.0]" name="threshold" 
+            optional="True" type="float"/>
+        <param default="None" label="-e/--entropy_threshold: Percent threshold for 
+            removing base positions with the highest entropy, expressed as a 
+            fraction between 0 and 1.  For example, if 0.10 were specified, the 
+            top 10% most entropic base positions would be filtered.  If this 
+            value is used, any lane mask supplied will be ignored.  Entropy filtering 
+            occurs after gap filtering. [default: None]" name="entropy_threshold" 
+            optional="True" type="float"/>
+    </inputs>
+
+    <outputs>
+        <data format="fasta" name="pfiltered.fasta" 
+            from_work_dir="filter_alignment_output/*pfiltered.fasta" 
+            label="filtered_alignement.fasta"/>
+    </outputs>
+
+    <tests>
+        <test>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This script should be applied to generate a useful tree when aligning against a 
+template alignment (e.g., with PyNAST). This script will remove positions which 
+are gaps in every sequence (common for PyNAST, as typical sequences cover only 
+200-400 bases, and they are being aligned against the full 16S gene). Additionally, 
+the user can supply a lanemask file, that defines which positions should included 
+when building the tree, and which should be ignored. Typically, this will differentiate 
+between non-conserved positions, which are uninformative for tree building, and 
+conserved positions which are informative for tree building. FILTERING ALIGNMENTS 
+WHICH WERE BUILT WITH PYNAST AGAINST THE GREENGENES CORE SET ALIGNMENT SHOULD BE 
+CONSIDERED AN ESSENTIAL STEP.
+
+The output of filter_alignment.py consists of a single FASTA file, which ends with 
+&quot;pfiltered.fasta&quot;, where the &quot;p&quot; stands for positional 
+filtering of the columns.
+    ]]>
+    </help>
+
+    <citations>
+        <expand macro="citations" />
+    </citations>
+</tool>