--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/masking.xml	Thu May 21 03:58:09 2015 -0400
@@ -0,0 +1,79 @@
+<tool id="vsearch_masking" name="VSearch masking" version="@VERSION@.0">
+    <description></description>
+    <macros>
+        <import>vsearch_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+    vsearch
+        @GENERAL@
+        #if $qmask != 'no':
+            --qmask $qmask
+        #end if
+        $hardmask
+        --maskfasta "$infile"
+        --output $outfile
+
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--maskfasta)" />
+        <expand macro="qmask" />
+        <expand macro="hardmask" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="db.fasta" ftype="fasta" />
+            <param name="qmask" value="dust"/>
+            <param name="hardmask" value="True"/>
+            <output name="outfile" file="masking_result1.fasta" ftype="fasta" />
+        </test>
+        <test>
+            <param name="infile" value="db.fasta" ftype="fasta" />
+            <param name="qmask" value="soft"/>
+            <param name="hardmask" value="True"/>
+            <output name="outfile" file="masking_result2.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+An input sequence can be composed of lower- or uppercase nucleotides. Lowercase nucleotides
+are silently set to uppercase before masking, unless the −−qmask soft option is used.
+Here are the results of combined masking options −−qmask (or −−dbmask for database sequences) and −−hardmask, assuming each input sequences contains both lower and uppercase nucleotides:
+
+===== ======== ================================================
+qmask hardmask action
+===== ======== ================================================
+none  off      no masking, all symbols uppercased
+none  on       no masking, all symbols uppercased
+dust  off      masked symbols lowercased, others uppercased
+dust  on       masked symbols changed to Ns, others uppercased
+soft  off      lowercase symbols masked, no case changes
+soft  on       lowercase symbols masked and changed to Ns
+===== ======== ================================================
+
+Masking options
+  --hardmask                  mask by replacing with N instead of lower case
+  --maskfasta FILENAME        mask sequences in the given FASTA file
+  --output FILENAME           output to specified FASTA file
+  --qmask                     mask seqs with "dust", "soft" or "none" method (dust)
+
+@EXTERNAL_DOCUMENTATION@
+
+-------
+
+@REFERENCES@
+
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>