--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/summary.seqs.xml	Fri May 19 05:24:16 2017 -0400
@@ -0,0 +1,73 @@
+<tool profile="16.07" id="mothur_summary_seqs" name="Summary.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Summarize the quality of sequences</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 &&
+
+        echo 'summary.seqs(
+            fasta=fasta.dat,
+            #if $name:
+                name=name.dat,
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/>
+        <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
+            <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test names input -->
+            <param name="fasta" value="amazon.unique.fasta"/>
+            <param name="name" value="amazon.names"/>
+            <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test count input -->
+            <param name="fasta" value="amazon.unique.fasta"/>
+            <param name="count" value="amazon.count_table"/>
+            <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
+
+
+.. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>