--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alimask.xml	Tue May 12 15:04:26 2015 -0400
@@ -0,0 +1,115 @@
+<?xml version="1.0"?>
+<tool id="hmmer_alimask" name="alimask" version="@WRAPPER_VERSION@.0">
+  <description>append modelmask line to a multiple sequence alignments</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <command><![CDATA[
+
+alimask
+
+#if $range_type.range_type_select == "model":
+    #set range = ','.join( [ "%s-%s" % (str($range.modelrangestart), str($range.modelrangeend)) for $range in $range_type.modelranges])
+    --modelrange $range
+#else
+    #set range = ','.join( [ "%s-%s" % (str($range.alirangestart), str($range.alirangeend)) for $range in $range_type.aliranges])
+    --alirange $range
+#end if
+
+@FORMAT_SELECTOR@
+@MCSS@
+@ARSWS@
+@SEED@
+
+$msafile
+$output
+      ]]></command>
+  <inputs>
+    <expand macro="input_msa" />
+    <conditional name="range_type">
+        <param name="range_type_select" type="select"
+            label="Input range coordinate basis">
+            <option value="model">Range in model coordinates</option>
+            <option value="ali">Range in alignment coordinates</option>
+        </param>
+        <when value="model">
+            <repeat min="1" name="modelranges" title="Model Ranges">
+                <param label="Model Range Start" name="modelrangestart" type="integer" value="10" />
+                <param label="Model Range End" name="modelrangeend" type="integer" value="20" />
+            </repeat>
+        </when>
+        <when value="ali">
+            <repeat min="1" name="aliranges" title="Alignment Ranges">
+                <param label="Alignment Range Start" name="alirangestart" type="integer" value="10" />
+                <param label="Alignment Range End" name="alirangeend" type="integer" value="20" />
+            </repeat>
+        </when>
+    </conditional>
+
+    <!-- TODO: support model2ali/ali2model as separate utilities? -->
+    <expand macro="format_selector"/>
+    <expand macro="mcss"/>
+    <expand macro="arsws"/>
+    <expand macro="seed"/>
+  </inputs>
+  <outputs>
+    <data format="stockholm" name="output" label="Output MSA"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="msafile" value="globins4.sto"/>
+      <param name="modelrangestart" value="10" />
+      <param name="modelrangeend" value="20" />
+      <expand macro="seed_test" />
+      <output name="output" file="globins-masked.sto" lines_diff="4"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+@HELP_PRE@
+
+alimask is used to apply a mask line to a multiple sequence alignment, based on
+provided alignment or model coordinates. When hmmbuild receives a masked
+alignment as input, it produces a profile model in which the emission
+probabilities at masked positions are set to match the background frequency,
+rather than being set based on observed frequencies in the alignment.
+Position-specific insertion and deletion rates are not altered, even in masked
+regions. alimask autodetects input format, and produces masked alignments in
+Stockholm format. <msafile> may contain only one sequence alignment.
+
+A common motivation for masking a region in an alignment is that the region
+contains a simple tandem repeat that is observed to cause an unacceptably high
+rate of false positive hits.
+
+In the simplest case, a mask range is given in coordinates relative to the
+input alignment, using --alirange <s>. However it is more often the case that
+the region to be masked has been identified in coordinates relative to the
+profile model (e.g. based on recognizing a simple repeat pattern in false hit
+alignments or in the HMM logo). Not all alignment columns are converted to
+match state positions in the profile (see the --symfrac flag for hmmbuild for
+discussion), so model positions do not necessarily match up to alignment column
+positions. To remove the burden of converting model positions to alignment
+positions, alimask accepts the mask range input in model coordinates as well,
+using --modelrange <s>. When using this flag, alimask determines which
+alignment positions would be identified by hmmbuild as match states, a process
+that requires that all hmmbuild flags impacting that decision be supplied to
+alimask. It is for this reason that many of the hmmbuild flags are also used by
+alimask.
+
+@HELP_PRE_OTH@
+
+**Ranges**
+
+Ranges are expressed as a hyphenated pair of integers, e.g. 12-40. Ranges can
+be expressed in terms of model coordinates or alignment coordinates.
+
+@FORMAT_SELECTOR_HELP@
+@MCSS_HELP@
+@ARSWS_HELP@
+@SEED_HELP@
+
+@ATTRIBUTION@
+]]></help>
+  <expand macro="citation"/>
+</tool>