--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/degap.seqs.xml	Fri Jun 24 16:29:07 2016 -0400
@@ -0,0 +1,48 @@
+<tool profile="16.07" id="mothur_degap_seqs" name="Degap.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Remove gap characters from sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+
+        echo 'degap.seqs(
+            fasta=fasta.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.ng.fasta" label="${tool.name} on ${on_string}: fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed.
+
+.. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs
+
+v1.21.0: Updated to Mothur 1.33
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>