Mercurial > repos > iuc > mothur_collect_shared

--- a/collect.shared.xml	Tue Sep 05 17:09:33 2017 -0400
+++ b/collect.shared.xml	Tue Mar 20 22:06:36 2018 -0400
@@ -7,29 +7,29 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@

-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&

-        echo 'collect.shared(
-            shared=otu.dat,
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $calc:
-                calc=${ str($calc).replace(",","-") },
-            #end if
-            #if $groups:
-                groups=${ str($groups).replace(",","-") },
-            #end if
-            freq=$freq,
-            all=true
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
-        && rm otu.dat  ## don't want this collected into datacollection
+echo 'collect.shared(
+    shared=otu.dat,
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $calc:
+        calc=${ str($calc).replace(",","-") },
+    #end if
+    #if $groups:
+        groups=${ str($groups).replace(",","-") },
+    #end if
+    freq=$freq,
+    all=true
+)'
+| 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.shared" label="shared - OTU Shared"/>
@@ -56,7 +56,9 @@
             <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
             <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
         </param>
-        <param name="freq" type="float" value="100" label="freq - indicates when to output your data" help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
+        <param name="freq" type="float" value="100" label="freq - indicates when to output your data"
+            help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -70,6 +72,7 @@
             <output_collection name="calcfiles" count="11">
                 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with group and label select and all calculators -->
@@ -80,11 +83,11 @@
             <output_collection name="calcfiles" count="39">
                 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[

 @MOTHUR_OVERVIEW@

@@ -94,7 +97,7 @@

 .. _calculators: https://www.mothur.org/wiki/Calculators
 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>
--- a/macros.xml	Tue Sep 05 17:09:33 2017 -0400
+++ b/macros.xml	Tue Mar 20 22:06:36 2018 -0400
@@ -1,11 +1,13 @@
 <macros>
+    <token name="@WRAPPER_VERSION@">1.39.5</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.36.1">mothur</requirement>
+            <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>
+            <yield/>
         </requirements>
     </xml>
     <xml name="version_command">
-        <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command>
+        <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command>
     </xml>
     <xml name="stdio">
         <stdio>
@@ -13,20 +15,10 @@
             <exit_code range="1:" level="fatal"/>
         </stdio>
     </xml>
-    <token name="@WRAPPER_VERSION@">1.36.1</token>
     <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
-    <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>
+    <!-- Input parameters -->
     <xml name="labeloptions">
         <options>
             <filter type="data_meta" ref="otu" key="labels"/>
@@ -78,9 +70,70 @@
         <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 ${on_string}: logfile"/>
+        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile">
+            <filter>savelog</filter>
+        </data>
     </xml>
+
+    <!-- Output file tests -->
     <xml name="logfile-test">
         <output name="logfile" ftype="txt">
             <assert_contents>
@@ -89,6 +142,101 @@
             </assert_contents>
         </output>
     </xml>
+
+    <xml name="test-accnos-format">
+        <!-- one or two columns -->
+        <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/>
+    </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>
Binary file test-data/Fasting_Example1.scrap.sff has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.0.03.pearson.otu.corr	Tue Mar 20 22:06:36 2018 -0400
@@ -0,0 +1,3829 @@
+OTUA	OTUB	pearsonCoef	Significance
+Otu02	Otu01	-1.000000	0.000000
+Otu03	Otu01	1.000000	0.000000
+Otu03	Otu02	-1.000000	0.000000
+Otu04	Otu01	-1.000000	0.000000
+Otu04	Otu02	1.000000	0.000000
+Otu04	Otu03	-1.000000	0.000000
+Otu05	Otu01	-nan	0.000000
+Otu05	Otu02	-nan	0.000000
+Otu05	Otu03	-nan	0.000000
+Otu05	Otu04	-nan	0.000000
+Otu06	Otu01	1.000000	0.000000
+Otu06	Otu02	-1.000000	0.000000
+Otu06	Otu03	1.000000	0.000000
+Otu06	Otu04	-1.000000	0.000000
+Otu06	Otu05	-nan	0.000000
+Otu07	Otu01	1.000000	0.000000
+Otu07	Otu02	-1.000000	0.000000
+Otu07	Otu03	1.000000	0.000000
+Otu07	Otu04	-1.000000	0.000000
+Otu07	Otu05	-nan	0.000000
+Otu07	Otu06	1.000000	0.000000
+Otu08	Otu01	1.000000	0.000000
+Otu08	Otu02	-1.000000	0.000000
+Otu08	Otu03	1.000000	0.000000
+Otu08	Otu04	-1.000000	0.000000
+Otu08	Otu05	-nan	0.000000
+Otu08	Otu06	1.000000	0.000000
+Otu08	Otu07	1.000000	0.000000
+Otu09	Otu01	1.000000	0.000000
+Otu09	Otu02	-1.000000	0.000000
+Otu09	Otu03	1.000000	0.000000
+Otu09	Otu04	-1.000000	0.000000
+Otu09	Otu05	-nan	0.000000
+Otu09	Otu06	1.000000	0.000000
+Otu09	Otu07	1.000000	0.000000
+Otu09	Otu08	1.000000	0.000000
+Otu10	Otu01	1.000000	0.000000
+Otu10	Otu02	-1.000000	0.000000
+Otu10	Otu03	1.000000	0.000000
+Otu10	Otu04	-1.000000	0.000000
+Otu10	Otu05	-nan	0.000000
+Otu10	Otu06	1.000000	0.000000
+Otu10	Otu07	1.000000	0.000000
+Otu10	Otu08	1.000000	0.000000
+Otu10	Otu09	1.000000	0.000000
+Otu11	Otu01	1.000000	0.000000
+Otu11	Otu02	-1.000000	0.000000
+Otu11	Otu03	1.000000	0.000000
+Otu11	Otu04	-1.000000	0.000000
+Otu11	Otu05	-nan	0.000000
+Otu11	Otu06	1.000000	0.000000
+Otu11	Otu07	1.000000	0.000000
+Otu11	Otu08	1.000000	0.000000
+Otu11	Otu09	1.000000	0.000000
+Otu11	Otu10	1.000000	0.000000
+Otu12	Otu01	1.000000	0.000000
+Otu12	Otu02	-1.000000	0.000000
+Otu12	Otu03	1.000000	0.000000
+Otu12	Otu04	-1.000000	0.000000
+Otu12	Otu05	-nan	0.000000
+Otu12	Otu06	1.000000	0.000000
+Otu12	Otu07	1.000000	0.000000
+Otu12	Otu08	1.000000	0.000000
+Otu12	Otu09	1.000000	0.000000
+Otu12	Otu10	1.000000	0.000000
+Otu12	Otu11	1.000000	0.000000
+Otu13	Otu01	1.000000	0.000000
+Otu13	Otu02	-1.000000	0.000000
+Otu13	Otu03	1.000000	0.000000
+Otu13	Otu04	-1.000000	0.000000
+Otu13	Otu05	-nan	0.000000
+Otu13	Otu06	1.000000	0.000000
+Otu13	Otu07	1.000000	0.000000
+Otu13	Otu08	1.000000	0.000000
+Otu13	Otu09	1.000000	0.000000
+Otu13	Otu10	1.000000	0.000000
+Otu13	Otu11	1.000000	0.000000
+Otu13	Otu12	1.000000	0.000000
+Otu14	Otu01	1.000000	0.000000
+Otu14	Otu02	-1.000000	0.000000
+Otu14	Otu03	1.000000	0.000000
+Otu14	Otu04	-1.000000	0.000000
+Otu14	Otu05	-nan	0.000000
+Otu14	Otu06	1.000000	0.000000
+Otu14	Otu07	1.000000	0.000000
+Otu14	Otu08	1.000000	0.000000
+Otu14	Otu09	1.000000	0.000000
+Otu14	Otu10	1.000000	0.000000
+Otu14	Otu11	1.000000	0.000000
+Otu14	Otu12	1.000000	0.000000
+Otu14	Otu13	1.000000	0.000000
+Otu15	Otu01	1.000000	0.000000
+Otu15	Otu02	-1.000000	0.000000
+Otu15	Otu03	1.000000	0.000000
+Otu15	Otu04	-1.000000	0.000000
+Otu15	Otu05	-nan	0.000000
+Otu15	Otu06	1.000000	0.000000
+Otu15	Otu07	1.000000	0.000000
+Otu15	Otu08	1.000000	0.000000
+Otu15	Otu09	1.000000	0.000000
+Otu15	Otu10	1.000000	0.000000
+Otu15	Otu11	1.000000	0.000000
+Otu15	Otu12	1.000000	0.000000
+Otu15	Otu13	1.000000	0.000000
+Otu15	Otu14	1.000000	0.000000
+Otu16	Otu01	1.000000	0.000000
+Otu16	Otu02	-1.000000	0.000000
+Otu16	Otu03	1.000000	0.000000
+Otu16	Otu04	-1.000000	0.000000
+Otu16	Otu05	-nan	0.000000
+Otu16	Otu06	1.000000	0.000000
+Otu16	Otu07	1.000000	0.000000
+Otu16	Otu08	1.000000	0.000000
+Otu16	Otu09	1.000000	0.000000
+Otu16	Otu10	1.000000	0.000000
+Otu16	Otu11	1.000000	0.000000
+Otu16	Otu12	1.000000	0.000000
+Otu16	Otu13	1.000000	0.000000
+Otu16	Otu14	1.000000	0.000000
+Otu16	Otu15	1.000000	0.000000
+Otu17	Otu01	1.000000	0.000000
+Otu17	Otu02	-1.000000	0.000000
+Otu17	Otu03	1.000000	0.000000
+Otu17	Otu04	-1.000000	0.000000
+Otu17	Otu05	-nan	0.000000
+Otu17	Otu06	1.000000	0.000000
+Otu17	Otu07	1.000000	0.000000
+Otu17	Otu08	1.000000	0.000000
+Otu17	Otu09	1.000000	0.000000
+Otu17	Otu10	1.000000	0.000000
+Otu17	Otu11	1.000000	0.000000
+Otu17	Otu12	1.000000	0.000000
+Otu17	Otu13	1.000000	0.000000
+Otu17	Otu14	1.000000	0.000000
+Otu17	Otu15	1.000000	0.000000
+Otu17	Otu16	1.000000	0.000000
+Otu18	Otu01	1.000000	0.000000
+Otu18	Otu02	-1.000000	0.000000
+Otu18	Otu03	1.000000	0.000000
+Otu18	Otu04	-1.000000	0.000000
+Otu18	Otu05	-nan	0.000000
+Otu18	Otu06	1.000000	0.000000
+Otu18	Otu07	1.000000	0.000000
+Otu18	Otu08	1.000000	0.000000
+Otu18	Otu09	1.000000	0.000000
+Otu18	Otu10	1.000000	0.000000
+Otu18	Otu11	1.000000	0.000000
+Otu18	Otu12	1.000000	0.000000
+Otu18	Otu13	1.000000	0.000000
+Otu18	Otu14	1.000000	0.000000
+Otu18	Otu15	1.000000	0.000000
+Otu18	Otu16	1.000000	0.000000
+Otu18	Otu17	1.000000	0.000000
+Otu19	Otu01	1.000000	0.000000
+Otu19	Otu02	-1.000000	0.000000
+Otu19	Otu03	1.000000	0.000000
+Otu19	Otu04	-1.000000	0.000000
+Otu19	Otu05	-nan	0.000000
+Otu19	Otu06	1.000000	0.000000
+Otu19	Otu07	1.000000	0.000000
+Otu19	Otu08	1.000000	0.000000
+Otu19	Otu09	1.000000	0.000000
+Otu19	Otu10	1.000000	0.000000
+Otu19	Otu11	1.000000	0.000000
+Otu19	Otu12	1.000000	0.000000
+Otu19	Otu13	1.000000	0.000000
+Otu19	Otu14	1.000000	0.000000
+Otu19	Otu15	1.000000	0.000000
+Otu19	Otu16	1.000000	0.000000
+Otu19	Otu17	1.000000	0.000000
+Otu19	Otu18	1.000000	0.000000
+Otu20	Otu01	1.000000	0.000000
+Otu20	Otu02	-1.000000	0.000000
+Otu20	Otu03	1.000000	0.000000
+Otu20	Otu04	-1.000000	0.000000
+Otu20	Otu05	-nan	0.000000
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+Otu20	Otu07	1.000000	0.000000
+Otu20	Otu08	1.000000	0.000000
+Otu20	Otu09	1.000000	0.000000
+Otu20	Otu10	1.000000	0.000000
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+Otu20	Otu17	1.000000	0.000000
+Otu20	Otu18	1.000000	0.000000
+Otu20	Otu19	1.000000	0.000000
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+Otu21	Otu03	1.000000	0.000000
+Otu21	Otu04	-1.000000	0.000000
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+Otu21	Otu07	1.000000	0.000000
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+Otu87	Otu82	1.000000	0.000000
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+Otu88	Otu37	-1.000000	0.000000
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+Otu88	Otu40	-1.000000	0.000000
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+Otu88	Otu46	-1.000000	0.000000
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+Otu88	Otu48	1.000000	0.000000
+Otu88	Otu49	1.000000	0.000000
+Otu88	Otu50	1.000000	0.000000
+Otu88	Otu51	1.000000	0.000000
+Otu88	Otu52	1.000000	0.000000
+Otu88	Otu53	1.000000	0.000000
+Otu88	Otu54	1.000000	0.000000
+Otu88	Otu55	1.000000	0.000000
+Otu88	Otu56	1.000000	0.000000
+Otu88	Otu57	1.000000	0.000000
+Otu88	Otu58	1.000000	0.000000
+Otu88	Otu59	1.000000	0.000000
+Otu88	Otu60	1.000000	0.000000
+Otu88	Otu61	1.000000	0.000000
+Otu88	Otu62	1.000000	0.000000
+Otu88	Otu63	1.000000	0.000000
+Otu88	Otu64	1.000000	0.000000
+Otu88	Otu65	1.000000	0.000000
+Otu88	Otu66	1.000000	0.000000
+Otu88	Otu67	1.000000	0.000000
+Otu88	Otu68	1.000000	0.000000
+Otu88	Otu69	1.000000	0.000000
+Otu88	Otu70	1.000000	0.000000
+Otu88	Otu71	1.000000	0.000000
+Otu88	Otu72	1.000000	0.000000
+Otu88	Otu73	1.000000	0.000000
+Otu88	Otu74	1.000000	0.000000
+Otu88	Otu75	1.000000	0.000000
+Otu88	Otu76	1.000000	0.000000
+Otu88	Otu77	1.000000	0.000000
+Otu88	Otu78	1.000000	0.000000
+Otu88	Otu79	1.000000	0.000000
+Otu88	Otu80	1.000000	0.000000
+Otu88	Otu81	1.000000	0.000000
+Otu88	Otu82	1.000000	0.000000
+Otu88	Otu83	1.000000	0.000000
+Otu88	Otu84	1.000000	0.000000
+Otu88	Otu85	1.000000	0.000000
+Otu88	Otu86	1.000000	0.000000
+Otu88	Otu87	1.000000	0.000000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.otus.accnos	Tue Mar 20 22:06:36 2018 -0400
@@ -0,0 +1,3 @@
+Otu01
+Otu17
+Otu42
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/esophagus.fn.shared	Tue Mar 20 22:06:36 2018 -0400
@@ -0,0 +1,12 @@
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+0.03	D	87	0	2	3	10	0	2	103	2	0	15	1	0	0	1	5	2	1	5	0	0	1	0	0	0	0	3	6	7	1	1	1	0	1	3	0	0	0	1	0	0	1	0	3	0	0	0	1	0	0	0	0	0	1	0	1	0	4	0	0	0	0	0	0	0	0	2	1	3	2	2	1	3	1	1	1	1	1	1	1	1	1	1	1	3	1	1	1
+0.05	B	74	12	23	34	14	3	47	1	1	8	6	1	1	2	5	1	3	2	12	3	2	1	1	4	1	2	1	1	1	2	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+0.05	C	74	14	2	38	42	0	12	2	10	7	1	0	0	2	0	5	3	2	3	4	0	0	1	29	0	0	2	0	2	14	0	0	0	7	0	0	0	0	4	2	2	2	11	1	3	3	1	8	4	1	1	1	1	4	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+0.05	D	74	0	2	18	10	2	115	2	0	1	3	0	1	5	2	1	0	0	1	0	0	0	6	7	1	1	2	0	1	4	0	0	0	1	0	0	1	3	0	1	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	2	1	2	2	1	3	1	1	1	1	1	1	1	1	1	1	3	1	1
+0.10	B	58	50	37	14	52	2	1	8	6	1	1	3	5	1	2	3	2	1	1	2	1	1	1	2	1	2	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+0.10	C	58	19	41	42	41	2	10	7	1	0	0	2	0	5	13	4	0	0	1	0	6	0	2	14	0	0	7	0	0	4	2	2	2	4	3	1	8	4	1	1	1	1	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+0.10	D	58	5	18	10	124	2	0	1	3	0	1	9	2	1	0	0	0	0	6	1	2	0	1	4	0	1	1	0	0	0	1	1	0	1	0	1	0	0	0	0	1	0	0	0	2	1	2	2	3	1	1	1	1	1	1	1	1	3	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samplebiom.biom1	Tue Mar 20 22:06:36 2018 -0400
@@ -0,0 +1,8668 @@
+{
+      "id":"otu.dat-0.03",
+      "format": "Biological Observation Matrix 0.9.1",
+      "format_url": "http://biom-format.org",
+      "type": "OTU table",
+      "generated_by": "mothur1.36.1",
+      "date": "Mon Jun 26 15:11:52 2017",
+      "rows":[
+            {"id":"Otu00001", "metadata":null},
+            {"id":"Otu00002", "metadata":null},
+            {"id":"Otu00003", "metadata":null},
+            {"id":"Otu00004", "metadata":null},
+            {"id":"Otu00005", "metadata":null},
+            {"id":"Otu00006", "metadata":null},
+            {"id":"Otu00007", "metadata":null},
+            {"id":"Otu00008", "metadata":null},
+            {"id":"Otu00009", "metadata":null},
+            {"id":"Otu00010", "metadata":null},
+            {"id":"Otu00011", "metadata":null},
+            {"id":"Otu00012", "metadata":null},
+            {"id":"Otu00013", "metadata":null},
+            {"id":"Otu00014", "metadata":null},
+            {"id":"Otu00015", "metadata":null},
+            {"id":"Otu00016", "metadata":null},
+            {"id":"Otu00017", "metadata":null},
+            {"id":"Otu00018", "metadata":null},
+            {"id":"Otu00019", "metadata":null},
+            {"id":"Otu00020", "metadata":null},
+            {"id":"Otu00021", "metadata":null},
+            {"id":"Otu00022", "metadata":null},
+            {"id":"Otu00023", "metadata":null},
+            {"id":"Otu00024", "metadata":null},
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