--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chop.seqs.xml	Fri Jun 24 17:35:55 2016 -0400
@@ -0,0 +1,75 @@
+<tool profile="16.07" id="mothur_chop_seqs" name="Chop.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Trim sequences to a specified length</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 "$fasta" fasta.dat &&
+        ln -s "$name" name.dat &&
+        ln -s "$group" group.dat &&
+        ln -s "$count" count.dat &&
+
+        echo 'chop.seqs(
+            fasta=fasta.dat,
+            numbases=$numbases,
+            keep=$keep,
+            countgaps=$countgaps,
+            short=$short,
+            #if $name:
+                name=name.dat,
+            #end if
+            #if $group:
+                group=group.dat,
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
+        <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
+        <param name="keep" type="select" label="keep - Part of the sequence to keep">
+            <option value="front">front</option>
+            <option value="back">back</option>
+        </param>
+        <param name="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/>
+        <param name="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/>
+        <param name="name" type="data" format="name" optional="true"  label="name file"/>
+        <param name="group" type="data" format="group" optional="true" label="group file"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.chop.fasta" label="${tool.name} on ${on_string}: chop.fasta"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names"/>
+            <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta" compare="contains"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences.
+
+.. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs
+
+v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>