--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make.lookup.xml	Fri Jun 24 16:38:35 2016 -0400
@@ -0,0 +1,101 @@
+<tool profile="16.07" id="mothur_make_lookup" name="Make.lookup" version="@WRAPPER_VERSION@.0">
+    <description>allows you to create custom lookup files for use with shhh.flows</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        #import re
+        ## create symlinks to input datasets
+        ln -s "$reference.template" reference.template.dat &&
+        ln -s "$flow" flow.dat &&
+        ln -s "$error" error.dat &&
+
+        echo 'make.lookup(
+            reference=reference.template.dat,
+            flow=flow.dat,
+            error=error.dat,
+            order=$order,
+            barcode=$re.sub("[^ACTG]","",str($barcode)),
+            key=$re.sub("[^ACTG]","",str($key)),
+            threshold=$threshold
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+    ]]></command>
+    <inputs>
+        <conditional name="reference">
+            <param name="source" type="select" label="Select Reference Template from" help="">
+                <option value="hist">History</option>
+                <option value="ref">Cached Reference</option>
+            </param>
+            <when value="ref">
+                <param name="template" type="select" label="reference - Select an alignment database " help="">
+                    <options from_data_table="mothur_aligndb"/>
+                </param>
+            </when>
+            <when value="hist">
+                <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
+            </when>
+        </conditional>
+        <param name="flow" type="data" format="motur.sff.flow" label="flow - provide file with flow data"/>
+        <param name="error" type="data" format="tabular" label="error - provide the error summary" help="this file is an output of seq.error tool"/>
+        <param name="order" type="select" label="order - flow order for nucleotides in the sequencer" help="default is A, was TACG. Also accepts B or I">
+            <option value="A" selected="true">A (TACG)</option>
+            <option value="B">B</option>
+            <option value="I">I</option>
+        </param>
+        <param name="barcode" type="text" value="AACCGTGTC" label="barcode - provide the barcode sequence"/>
+        <param name="key" type="text" value="TCAG" label="key - provide the key sequence"/>
+        <param name="threshold" type="integer" value="10000" min="0" label="threshold - " help=""/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="lookup_out" format="txt" from_work_dir="flow*.lookup" label="${tool.name} on ${on_string}: lookup"/>
+    </outputs>
+    <tests>
+        <test><!-- test with defaults -->
+            <param name="source" value="hist"/>
+            <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
+            <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
+            <param name="error" value="Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary" ftype="tabular"/>
+            <output name="lookup_out" ftype="txt">
+                <assert_contents>
+                    <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test sanitizers -->
+            <param name="source" value="hist"/>
+            <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
+            <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
+            <param name="error" value="Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary" ftype="tabular"/>
+            <param name="barcode" value="XAXAXCXCXGXTXGXTXC"/><!-- should be converted to default value -->
+            <param name="key" value="XTXCXAXGX"/><!-- should be converted to default value -->
+            <output name="lookup_out" ftype="txt">
+                <assert_contents>
+                    <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The make.lookup_ allows you to create custom lookup files for use with shhh.flows.
+
+.. _make.lookup: http://www.mothur.org/wiki/Make.lookup
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1128/AEM.01541-09</citation>
+    </citations>
+</tool>