--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/align.check.xml	Fri May 19 05:36:43 2017 -0400
@@ -0,0 +1,87 @@
+<tool profile="16.07" id="mothur_align_check" name="Align.check" version="@WRAPPER_VERSION@.0">
+    <description>Calculate the number of potentially misaligned bases</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+        ln -s "$name" name.dat &&
+        ln -s "$count" count.dat &&
+        ln -s "$map" map.dat &&
+
+        echo 'align.check(
+            fasta=fasta.dat,
+            #if $name:
+                name=name.dat,
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            map=map.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+        <inputs>
+            <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/>
+            <conditional name="ss">
+                <param name="source" label="Select Secondary Structure Map from" type="select">
+                    <option value="cached">Cached Secondary Structure Maps</option>
+                    <option value="history">Your History</option>
+                </param>
+                <when value="cached">
+                    <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
+                        <options from_data_table="mothur_map">
+                        </options>
+                    </param>
+                </when>
+                <when value="history">
+                    <param name="map" format="mothur.map" type="data" label="Secondary Structure Map"/>
+                </when>
+            </conditional>
+            <param name="count" type="data" format="mothur.count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/>
+            <param name="name" type="data" format="mothur.names" label="names file" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/>
+        </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_file" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/>
+    </outputs>
+    <tests>
+        <test><!-- test with defaults -->
+            <param name="fasta" value="amazon.align_head_short"/>
+            <param name="source" value="history"/>
+            <param name="map" value="silva.ss.map.head"/>
+            <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with names file -->
+            <param name="fasta" value="amazon.align_head_short"/>
+            <param name="source" value="history"/>
+            <param name="map" value="silva.ss.map.head"/>
+            <param name="name" value="amazon.align_head.names"/>
+            <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map_.  If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs.
+
+.. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map
+.. _align.check: https://www.mothur.org/wiki/Align.check
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>