--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collect.single.xml	Fri May 19 05:17:32 2017 -0400
@@ -0,0 +1,111 @@
+<tool profile="16.07" id="mothur_collect_single" name="Collect.single" version="@WRAPPER_VERSION@.0">
+    <description>Generate collector's curves for OTUs</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 "$otu" otu.dat &&
+
+        echo 'collect.single(
+            #if $otu.is_of_type("mothur.rabund"):
+                rabund=otu.dat,
+            #elif $otu.is_of_type("mothur.sabund"):
+                sabund=otu.dat,
+            #elif $otu.is_of_type("mothur.shared"):
+                shared=otu.dat,
+            #elif $otu.is_of_type("mothur.list"):
+                list=otu.dat,
+            #end if
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            calc=${ str($calc).replace(",","-") },
+            abund=$abund,
+            freq=$freq
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+        && rm otu.dat  ## don't want this collected into datacollection
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
+        <param name="label" type="select" label="label - OTU Labels" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
+            <option value="ace" selected="true">ace - Community richness the ACE estimator</option>
+            <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
+            <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option>
+            <option value="jack" selected="true">jack - Community richness the jackknife estimator</option>
+            <option value="sobs" selected="true">sobs - Community richness the observed richness</option>
+            <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option>
+            <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option>
+            <option value="heip">heip - Community evenness Heip's metric of community evenness</option>
+            <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option>
+            <option value="bergerparker">bergerparker - Community diversity the Berger-Parker index</option>
+            <option value="coverage">coverage - Community diversity the sampling coverage </option>
+            <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option>
+            <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option>
+            <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
+            <option value="qstat">qstat - Community diversity the Q statistic</option>
+            <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option>
+            <option value="npshannon" selected="true">npshannon - Community diversity the non-parametric Shannon index</option>
+            <option value="boneh">boneh - Estimator Boneh's estimator</option>
+            <option value="efron">efron - Estimator Efron's estimator</option>
+            <option value="shen">shen - Estimator Shen's estimator</option>
+            <option value="solow">solow - Estimator Solow's estimator</option>
+            <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log series distribution</option>
+            <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option>
+            <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</option>
+            <option value="nseqs">nseqs - Utility the number of sequences in a sample</option>
+        </param>
+        <param name="abund" type="integer" value="10" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/>
+        <param name="freq" type="float" value="100" min="0" label="freq - frequency for output (default is every 100 sequences)" help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
+            <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test default settings -->
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <output_collection name="calcfiles" count="7">
+                <element name="shannon" md5="0a9c8a52f89898c3b7b7b2dfa24a4521" ftype="tabular"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with label select and all calculators -->
+            <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
+            <param name="label" value="0.36,0.38,0.41"/>
+            <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,bergerparker,coverage,goodscoverage,simpson,invsimpson,qstat,shannon,npshannon,boneh,efron,shen,solow,logseries,geometric,bstick,nseqs"/>
+            <output_collection name="calcfiles" count="25">
+                <element name="bstick" md5="a38d430c52768efca597e5b41fc1d84b" ftype="tabular"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+
+**Command Documentation**
+
+The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
+
+.. _calculators: https://www.mothur.org/wiki/Calculators
+.. _collect.single: https://www.mothur.org/wiki/Collect.single
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>