--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin.seqs.xml	Fri May 19 05:43:37 2017 -0400
@@ -0,0 +1,90 @@
+<tool profile="16.07" id="mothur_bin_seqs" name="Bin.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Order Sequences by OTU</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 "$name" name.dat &&
+        ln -s "$group" group.dat &&
+        ln -s "$fasta" fasta.dat &&
+        ln -s "$otu" otu.dat &&
+        ln -s "$count" count.dat &&
+
+        echo 'bin.seqs(
+            #if $name:
+                name=name.dat,
+            #end if
+            #if $group:
+                group=group.dat,
+            #end if
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            fasta=fasta.dat,
+            list=otu.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
+        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test with defaults -->
+            <param name="otu" value="amazon.an.list"/>
+            <param name="fasta" value="amazon.fasta"/>
+            <output_collection name="fastafiles" count="36">
+                <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with group and name file and label select -->
+            <param name="otu" value="amazon.an.list"/>
+            <param name="fasta" value="amazon.fasta"/>
+            <param name="name" value="amazon.names"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="label" value="0.03,0.05,0.22"/>
+            <output_collection name="fastafiles" count="3">
+                <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.
+
+.. _list_file: https://www.mothur.org/wiki/List_file
+.. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>