--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 20 21:54:35 2018 -0400
@@ -0,0 +1,246 @@
+<macros>
+    <token name="@WRAPPER_VERSION@">1.39.5</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <regex match="\[ERROR\]" source="stdout" level="fatal"/>
+            <exit_code range="1:" level="fatal"/>
+        </stdio>
+    </xml>
+    <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
+
+
+    <!-- Input parameters -->
+    <xml name="labeloptions">
+        <options>
+            <filter type="data_meta" ref="otu" key="labels"/>
+        </options>
+    </xml>
+    <xml name="calc-common">
+        <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first -->
+        <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+        <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+        <option value="canberra">canberra - Community Structure Similarity</option>
+        <option value="gower">gower - Community Structure Similarity</option>
+        <option value="hamming">hamming - Community Membership Similarity</option>
+        <option value="hellinger">hellinger - Community Structure Similarity</option>
+        <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+        <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+        <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+        <option value="jsd">jsd</option>
+        <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
+        <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
+        <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
+        <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
+        <option value="manhattan">manhattan - Community Structure Similarity</option>
+        <option value="memchi2">memchi2 - Community Membership Similarity</option>
+        <option value="memchord">memchord - Community Membership Similarity</option>
+        <option value="memeuclidean">memeuclidean - Community Membership Similarity</option>
+        <option value="mempearson">mempearson - Community Membership Similarity</option>
+        <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+        <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
+        <option value="odum">odum - Community Structure Similarity</option>
+        <option value="rjsd">rjsd</option>
+        <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
+        <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
+        <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
+        <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
+        <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
+        <option value="soergel">soergel - Community Structure Similarity</option>
+        <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+        <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+        <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+        <option value="spearman">spearman - Community Structure Similarity</option>
+        <option value="speciesprofile">speciesprofile - Community Structure Similarity</option>
+        <option value="structchi2">structchi2 - Community Structure Similarity</option>
+        <option value="structchord">structchord - Community Structure Similarity</option>
+        <option value="structeuclidean">structeuclidean - Community Structure Similarity</option>
+        <option value="structkulczynski">structkulczynski - Community Structure Similarity</option>
+        <option value="structpearson">structpearson - Community Structure Similarity</option>
+        <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+        <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
+        <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
+        <yield/>
+    </xml>
+
+    <!-- CLUSTERING -->
+    <xml name="param-clustermethods">
+        <param argument="method" type="select" label="Clustering Method">
+            <option value="opti" selected="true">Opticlust method</option>
+            <option value="furthest">Furthest neighbor</option>
+            <option value="nearest">Nearest neighbor</option>
+            <option value="average">Average neighbor</option>
+            <yield/>
+        </param>
+    </xml>
+    <xml name="option-vsearch-clustermethods">
+        <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option>
+        <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option>
+    </xml>
+    <xml name="params-opticlust">
+        <param argument="metric" type="select" label="metric - select the metric in the opticluster method"
+            help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn),
+            false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score),
+            accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.">
+            <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option>
+            <option value="sens">Sensitivity</option>
+            <option value="spec">specificity</option>
+            <option value="tptn">true positives + true negatives</option>
+            <option value="fpfn">false positives + false negatives</option>
+            <option value="tp">true positives</option>
+            <option value="tn">true negative</option>
+            <option value="fp">false positive</option>
+            <option value="fn">false negative</option>
+            <option value="f1score">f1score</option>
+            <option value="accuracy">accuracy</option>
+            <option value="ppv">positive predictive value</option>
+            <option value="npv">negative predictive value</option>
+            <option value="fdr">false discovery rate</option>
+        </param>
+        <param argument="initialize" type="select" label="Initial randomization"
+            help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu">
+            <option value="singleton" selected="true">Singleton</option>
+            <option value="oneotu">Oneotu</option>
+        </param>
+        <param argument="delta" type="float" value="0.0001" label="set the stable value for the metric in the opticluster method"
+            help="The delta parameter allows to set the stable value for the metric in the opticluster method. To reach a full convergence, set delta=0."/>
+        <param argument="iters" type="integer" value="100" label="Maximum number of iterations"/>
+    </xml>
+    <xml name="param-output">
+        <param argument="output" type="select" label="Tax summary output type"
+            help="The detail format outputs the totals at each level, where as the simple format outputs the highest level">
+            <option value="simple" selected="true">simple</option>
+            <option value="detail">detail</option>
+        </param>
+    </xml>
+    <xml name="param-printlevel">
+        <param argument="printlevel" type="integer" value="-1" min="-1" label="Print level" help="specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level" />
+    </xml>
+    <xml name="param-savelog">
+        <param name="savelog" type="boolean" checked="false" label="Output logfile?"/>
+    </xml>
+    <xml name="logfile-output">
+        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile">
+            <filter>savelog</filter>
+        </data>
+    </xml>
+
+    <!-- Output file tests -->
+    <xml name="logfile-test">
+        <output name="logfile" ftype="txt">
+            <assert_contents>
+                <has_text text="mothur"/>
+                <has_text text="@WRAPPER_VERSION@"/>
+            </assert_contents>
+        </output>
+    </xml>
+
+    <xml name="test-accnos-format">
+        <!-- one or two columns -->
+        <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/>
+    </xml>
+    <xml name="test-align-format">
+        <has_line_matching expression="^>.+$"/>
+        <has_line_matching expression="^[ACTG\-\.]+$"/>
+    </xml>
+    <xml name="test-aligncheck-format">
+        <has_n_columns n="9"/>
+        <has_line_matching expression="^name\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs$"/>
+    </xml>
+    <xml name="test-alignreport-format">
+        <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&amp;Template$"/>
+    </xml>
+    <xml name="test-axes-format">
+        <has_line_matching expression="^group(\taxis\d+)+$"/>
+    </xml>
+    <xml name="test-chimera-format">
+        <has_line_matching expression="Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN"/>
+    </xml>
+    <xml name="test-column-format">
+        <has_n_columns n="3"/>
+        <has_line_matching expression="^[\w\d\-]+\t[\w\d\-]+\t[\d\.]+$"/>
+    </xml>
+    <xml name="test-contigsreport-format">
+        <has_n_columns n="7"/>
+        <has_line_matching expression="^Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns$"/>
+    </xml>
+    <xml name="test-count-format">
+        <has_line_matching expression="^Representative_Sequence\ttotal(\t\w+)*$"/>
+        <has_line_matching expression="^\w+(\t\d+)+(\s)*$"/>
+    </xml>
+    <xml name="test-dist-format">
+        <has_line_matching expression="^[ \t]*\d+$"/>
+        <has_line_matching expression="^[\w\d\-]+(\t[\d\.]+)+\s?$"/>
+    </xml>
+    <xml name="test-fasta-format">
+        <has_line_matching expression="^>.+$"/>
+        <has_line_matching expression="^[ACTGN-]+$"/>
+    </xml>
+    <xml name="test-fastq-format">
+        <has_line_matching expression="^@.+$"/>
+        <has_line_matching expression="^[ACTGN]+$"/>
+        <has_line_matching expression="^\+$"/>
+    </xml>
+    <xml name="test-group-format">
+        <has_line_matching expression="^Representative_Sequence\ttotal(\t[\w\d\-]+)+$"/>
+        <has_line_matching expression="^[\w\d\-]+(\t\d+)+$"/>
+    </xml>
+    <xml name="test-list-format">
+        <has_line_matching expression="^label\tnumOtus(\tOtu\d+)+$"/>
+        <has_line_matching expression="^(unique|0\.\d+)\t\d+(\t[\w\d\-,]+)+$"/>
+    </xml>
+    <xml name="test-names-format">
+        <has_line_matching expression="^[a-zA-Z0-9]+\t[a-zA-Z0-9]+$"/>
+    </xml>
+    <xml name="test-qfile-format">
+        <has_line_matching expression="^(\d+ )+$"/>
+        <has_line_matching expression="^>.+$"/>
+    </xml>
+    <xml name="test-rabund-format">
+        <has_line_matching expression="^(unique|0\.\d+)(\t\d+\.?\d*)+$"/>
+    </xml>
+    <xml name="test-sabund-format">
+        <has_line_matching expression="^(unique|0\.\d+)(\t\d+)+$"/>
+    </xml>
+    <xml name="test-sensspec-format">
+        <has_n_columns n="14"/>
+        <has_line_matching expression="^label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\t\w+\tf1score$"/>
+    </xml>
+    <xml name="test-shared-format">
+        <has_line_matching expression="^label\tGroup\tnumOtus(\t(Otu|rareOTUs|.*OTU.*)\d+)+$"/>
+    </xml>
+    <xml name="test-taxonomy-format">
+        <has_n_columns n="3"/>
+        <has_line_matching expression="^OTU\tSize\tTaxonomy$"/>
+    </xml>
+    <xml name="test-taxsummary-format">
+        <has_line_matching expression="^((taxlevel\trankID\ttaxon\tdaughterlevels\ttotal(\t[\w\d\-]+)*)|(taxonomy\ttotal(\t[\w\d]+)*))$"/>
+    </xml>
+    <!-- backmatter -->
+    <token name="@MOTHUR_OVERVIEW@">
+<![CDATA[
+
+**Mothur Overview**
+
+Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
+
+.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
+
+]]>
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1128/AEM.01541-09</citation>
+            <yield/>
+        </citations>
+    </xml>
+</macros>