changeset 2:6f2cdccbfa48 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:08:08 -0400
parents 2834e2dd0d61
children f53e9df3e598
files cluster.xml macros.xml test-data/Fasting_Example1.scrap.sff test-data/amazon.an.0.03.pearson.otu.corr test-data/amazon.otus.accnos test-data/esophagus.fn.shared test-data/samplebiom.biom1 test-data/stool_small.count_table test-data/stool_small.denovo.vsearch.accnos test-data/stool_small.names test-data/stool_small.unique.fasta test-data/stool_small.vsearch.chimeras
diffstat 12 files changed, 13039 insertions(+), 69 deletions(-) [+]
line wrap: on
line diff
--- a/cluster.xml	Tue Sep 05 17:13:06 2017 -0400
+++ b/cluster.xml	Tue Mar 20 22:08:08 2018 -0400
@@ -3,66 +3,89 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
+    <expand macro="requirements">
+        <requirement type="package" version="2.6.0">vsearch</requirement>
+    </expand>
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$matrix.dist" matrix.dist.dat &&
-        ln -s "$matrix.name" matrix.name.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$matrix.dist' matrix.dist.dat &&
+ln -s '$matrix.name' matrix.name.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'cluster(
-            #if $matrix.format == "phylip":
-                phylip=matrix.dist.dat,
-            #else
-                column=matrix.dist.dat,
-            #end if
-            #if $matrix.name:
-                name=matrix.name.dat,
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            hard=$hard,
-            #if float($cutoff) > 0.0:
-                cutoff=$cutoff,
-            #end if
-            precision=$precision,
-            sim=$sim,
-            method=$method
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'cluster(
+    #if $matrix.format == "phylip":
+        phylip=matrix.dist.dat,
+    #else
+        column=matrix.dist.dat,
+    #end if
+    #if $matrix.name:
+        name=matrix.name.dat,
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    #if float($cutoff) > 0.0:
+        cutoff=$cutoff,
+    #end if
+    #if $select_method.method =="opti":
+        metric=$select_method.metric,
+        initialize=$select_method.initialize,
+        delta=$select_method.delta,
+        iters=$select_method.iters,
+    #end if
+    precision=$precision,
+    sim=$sim,
+    method=$select_method.method
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="matrix">
-            <param name="format" type="select" label="Select a Distance Matrix Format" help="">
+            <param name="format" type="select" label="Cluster based on" help="">
                 <option value="column">Pairwise Column Matrix</option>
                 <option value="phylip">Phylip Distance Matrix</option>
+                <option value="fasta">Fasta (VSEARCH)</option>
             </param>
             <when value="column">
-                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
-                <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+                <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
+                <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
             </when>
             <when value="phylip">
-                <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
-                <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+                <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+                <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
+            </when>
+            <when value="fasta">
+                <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
             </when>
         </conditional>
-        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
-        <param name="method" type="select" label="method - Select a Clustering Method" help="">
-            <option value="furthest">Furthest neighbor</option>
-            <option value="nearest">Nearest neighbor</option>
-            <option value="average" selected="true">Average neighbor</option>
-            <option value="weighted">Weighted</option>
-        </param>
-        <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0.0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
-        <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
-        <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
+        <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <conditional name="select_method">
+            <expand macro="param-clustermethods">
+                <expand macro="option-vsearch-clustermethods"/>
+            </expand>
+            <when value="furthest"/>
+            <when value="nearest"/>
+            <when value="average"/>
+            <when value="agc">
+                <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
+            </when>
+            <when value="dgc">
+                <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
+            </when>
+            <when value="opti">
+                <expand macro="params-opticlust"/>
+            </when>
+        </conditional>
+        <param argument="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0.0"
+            help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
+        <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
+            help="Set higher precision for longer genome scale sequence lengths">
             <option value="10">.1</option>
             <option value="100" selected="true">.01</option>
             <option value="1000">.001</option>
@@ -70,7 +93,8 @@
             <option value="100000">.00001</option>
             <option value="1000000">.000001</option>
         </param>
-        <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
+        <param argument="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -82,23 +106,76 @@
         <test><!-- test with phylip input -->
             <param name="format" value="phylip"/>
             <param name="dist" value="amazon.dist"/>
-            <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
-            <output name="sabund" file="amazon.an.sabund" ftype="mothur.sabund"/>
-            <output name="otulist" md5="a6bf2a6ef7950b3ee2aa5bff4a662b6d" ftype="mothur.list"/>
+            <output name="rabund" ftype="mothur.rabund">
+                <assert_contents>
+                    <has_line_matching expression="^0\.03(\t\d+)+$"/>
+                </assert_contents>
+            </output>
+            <output name="sabund" ftype="mothur.sabund">
+                <assert_contents>
+                    <has_line_matching expression="^0\.03(\t\d+)+$"/>
+                </assert_contents>
+            </output>
+            <output name="otulist" ftype="mothur.list">
+                <assert_contents>
+                    <expand macro="test-list-format"/>
+                    <has_text text="0.03"/>
+                    <has_text text="U68688"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with column input -->
             <param name="format" value="column"/>
             <param name="dist" value="amazon.pair.dist"/>
             <param name="name" value="amazon.names"/>
-            <output name="rabund" md5="ec88216404729d0f4a0463e50e60c9ad" ftype="mothur.rabund"/>
-            <output name="sabund" md5="f2c714531430b98d8cdfd3497468eec2" ftype="mothur.sabund"/>
-            <output name="otulist" md5="1769463ed0b6680babe5801bf9c0a85c" ftype="mothur.list"/>
+            <output name="rabund" ftype="mothur.rabund">
+                <assert_contents>
+                    <has_line_matching expression="^0\.03(\t\d+)+$"/>
+                </assert_contents>
+            </output>
+            <output name="sabund" ftype="mothur.sabund">
+                <assert_contents>
+                    <has_line_matching expression="^0\.03(\t\d+)+$"/>
+                </assert_contents>
+            </output>
+            <output name="otulist" ftype="mothur.list">
+                <assert_contents>
+                    <expand macro="test-list-format"/>
+                    <has_text text="0.03"/>
+                    <has_text text="U68688"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with column input -->
+            <param name="format" value="column"/>
+            <param name="dist" value="amazon.pair.dist"/>
+            <param name="name" value="amazon.names"/>
+            <output name="rabund" ftype="mothur.rabund">
+                <assert_contents>
+                    <has_line_matching expression="^0\.03(\t\d+)+$"/>
+                </assert_contents>
+            </output>
+            <output name="sabund" ftype="mothur.sabund">
+                <assert_contents>
+                    <has_line_matching expression="^0\.03(\t\d+)+$"/>
+                </assert_contents>
+            </output>
+            <output name="otulist" ftype="mothur.list">
+                <assert_contents>
+                    <expand macro="test-list-format"/>
+                    <has_text text="0.03"/>
+                    <has_text text="U68688"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -114,7 +191,6 @@
 .. _sabund: https://www.mothur.org/wiki/Sabund_file
 .. _cluster: https://www.mothur.org/wiki/Cluster
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>
--- a/macros.xml	Tue Sep 05 17:13:06 2017 -0400
+++ b/macros.xml	Tue Mar 20 22:08:08 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 22:08:08 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
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+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
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+Otu16	Otu03	1.000000	0.000000
+Otu16	Otu04	-1.000000	0.000000
+Otu16	Otu05	-nan	0.000000
+Otu16	Otu06	1.000000	0.000000
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+Otu17	Otu01	1.000000	0.000000
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+Otu17	Otu04	-1.000000	0.000000
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+Otu17	Otu12	1.000000	0.000000
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+Otu17	Otu14	1.000000	0.000000
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+Otu17	Otu16	1.000000	0.000000
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+Otu18	Otu04	-1.000000	0.000000
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+Otu18	Otu16	1.000000	0.000000
+Otu18	Otu17	1.000000	0.000000
+Otu19	Otu01	1.000000	0.000000
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+Otu19	Otu04	-1.000000	0.000000
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+Otu33	Otu01	1.000000	0.000000
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+Otu33	Otu04	-1.000000	0.000000
+Otu33	Otu05	-nan	0.000000
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+Otu85	Otu75	1.000000	0.000000
+Otu85	Otu76	1.000000	0.000000
+Otu85	Otu77	1.000000	0.000000
+Otu85	Otu78	1.000000	0.000000
+Otu85	Otu79	1.000000	0.000000
+Otu85	Otu80	1.000000	0.000000
+Otu85	Otu81	1.000000	0.000000
+Otu85	Otu82	1.000000	0.000000
+Otu85	Otu83	1.000000	0.000000
+Otu85	Otu84	1.000000	0.000000
+Otu86	Otu01	-1.000000	0.000000
+Otu86	Otu02	1.000000	0.000000
+Otu86	Otu03	-1.000000	0.000000
+Otu86	Otu04	1.000000	0.000000
+Otu86	Otu05	-nan	0.000000
+Otu86	Otu06	-1.000000	0.000000
+Otu86	Otu07	-1.000000	0.000000
+Otu86	Otu08	-1.000000	0.000000
+Otu86	Otu09	-1.000000	0.000000
+Otu86	Otu10	-1.000000	0.000000
+Otu86	Otu11	-1.000000	0.000000
+Otu86	Otu12	-1.000000	0.000000
+Otu86	Otu13	-1.000000	0.000000
+Otu86	Otu14	-1.000000	0.000000
+Otu86	Otu15	-1.000000	0.000000
+Otu86	Otu16	-1.000000	0.000000
+Otu86	Otu17	-1.000000	0.000000
+Otu86	Otu18	-1.000000	0.000000
+Otu86	Otu19	-1.000000	0.000000
+Otu86	Otu20	-1.000000	0.000000
+Otu86	Otu21	-1.000000	0.000000
+Otu86	Otu22	-1.000000	0.000000
+Otu86	Otu23	-1.000000	0.000000
+Otu86	Otu24	1.000000	0.000000
+Otu86	Otu25	-1.000000	0.000000
+Otu86	Otu26	-1.000000	0.000000
+Otu86	Otu27	-1.000000	0.000000
+Otu86	Otu28	-1.000000	0.000000
+Otu86	Otu29	-1.000000	0.000000
+Otu86	Otu30	-1.000000	0.000000
+Otu86	Otu31	-1.000000	0.000000
+Otu86	Otu32	-1.000000	0.000000
+Otu86	Otu33	-1.000000	0.000000
+Otu86	Otu34	-1.000000	0.000000
+Otu86	Otu35	-1.000000	0.000000
+Otu86	Otu36	-1.000000	0.000000
+Otu86	Otu37	-1.000000	0.000000
+Otu86	Otu38	-1.000000	0.000000
+Otu86	Otu39	-1.000000	0.000000
+Otu86	Otu40	-1.000000	0.000000
+Otu86	Otu41	-1.000000	0.000000
+Otu86	Otu42	-1.000000	0.000000
+Otu86	Otu43	-1.000000	0.000000
+Otu86	Otu44	-1.000000	0.000000
+Otu86	Otu45	-1.000000	0.000000
+Otu86	Otu46	-1.000000	0.000000
+Otu86	Otu47	1.000000	0.000000
+Otu86	Otu48	1.000000	0.000000
+Otu86	Otu49	1.000000	0.000000
+Otu86	Otu50	1.000000	0.000000
+Otu86	Otu51	1.000000	0.000000
+Otu86	Otu52	1.000000	0.000000
+Otu86	Otu53	1.000000	0.000000
+Otu86	Otu54	1.000000	0.000000
+Otu86	Otu55	1.000000	0.000000
+Otu86	Otu56	1.000000	0.000000
+Otu86	Otu57	1.000000	0.000000
+Otu86	Otu58	1.000000	0.000000
+Otu86	Otu59	1.000000	0.000000
+Otu86	Otu60	1.000000	0.000000
+Otu86	Otu61	1.000000	0.000000
+Otu86	Otu62	1.000000	0.000000
+Otu86	Otu63	1.000000	0.000000
+Otu86	Otu64	1.000000	0.000000
+Otu86	Otu65	1.000000	0.000000
+Otu86	Otu66	1.000000	0.000000
+Otu86	Otu67	1.000000	0.000000
+Otu86	Otu68	1.000000	0.000000
+Otu86	Otu69	1.000000	0.000000
+Otu86	Otu70	1.000000	0.000000
+Otu86	Otu71	1.000000	0.000000
+Otu86	Otu72	1.000000	0.000000
+Otu86	Otu73	1.000000	0.000000
+Otu86	Otu74	1.000000	0.000000
+Otu86	Otu75	1.000000	0.000000
+Otu86	Otu76	1.000000	0.000000
+Otu86	Otu77	1.000000	0.000000
+Otu86	Otu78	1.000000	0.000000
+Otu86	Otu79	1.000000	0.000000
+Otu86	Otu80	1.000000	0.000000
+Otu86	Otu81	1.000000	0.000000
+Otu86	Otu82	1.000000	0.000000
+Otu86	Otu83	1.000000	0.000000
+Otu86	Otu84	1.000000	0.000000
+Otu86	Otu85	1.000000	0.000000
+Otu87	Otu01	-1.000000	0.000000
+Otu87	Otu02	1.000000	0.000000
+Otu87	Otu03	-1.000000	0.000000
+Otu87	Otu04	1.000000	0.000000
+Otu87	Otu05	-nan	0.000000
+Otu87	Otu06	-1.000000	0.000000
+Otu87	Otu07	-1.000000	0.000000
+Otu87	Otu08	-1.000000	0.000000
+Otu87	Otu09	-1.000000	0.000000
+Otu87	Otu10	-1.000000	0.000000
+Otu87	Otu11	-1.000000	0.000000
+Otu87	Otu12	-1.000000	0.000000
+Otu87	Otu13	-1.000000	0.000000
+Otu87	Otu14	-1.000000	0.000000
+Otu87	Otu15	-1.000000	0.000000
+Otu87	Otu16	-1.000000	0.000000
+Otu87	Otu17	-1.000000	0.000000
+Otu87	Otu18	-1.000000	0.000000
+Otu87	Otu19	-1.000000	0.000000
+Otu87	Otu20	-1.000000	0.000000
+Otu87	Otu21	-1.000000	0.000000
+Otu87	Otu22	-1.000000	0.000000
+Otu87	Otu23	-1.000000	0.000000
+Otu87	Otu24	1.000000	0.000000
+Otu87	Otu25	-1.000000	0.000000
+Otu87	Otu26	-1.000000	0.000000
+Otu87	Otu27	-1.000000	0.000000
+Otu87	Otu28	-1.000000	0.000000
+Otu87	Otu29	-1.000000	0.000000
+Otu87	Otu30	-1.000000	0.000000
+Otu87	Otu31	-1.000000	0.000000
+Otu87	Otu32	-1.000000	0.000000
+Otu87	Otu33	-1.000000	0.000000
+Otu87	Otu34	-1.000000	0.000000
+Otu87	Otu35	-1.000000	0.000000
+Otu87	Otu36	-1.000000	0.000000
+Otu87	Otu37	-1.000000	0.000000
+Otu87	Otu38	-1.000000	0.000000
+Otu87	Otu39	-1.000000	0.000000
+Otu87	Otu40	-1.000000	0.000000
+Otu87	Otu41	-1.000000	0.000000
+Otu87	Otu42	-1.000000	0.000000
+Otu87	Otu43	-1.000000	0.000000
+Otu87	Otu44	-1.000000	0.000000
+Otu87	Otu45	-1.000000	0.000000
+Otu87	Otu46	-1.000000	0.000000
+Otu87	Otu47	1.000000	0.000000
+Otu87	Otu48	1.000000	0.000000
+Otu87	Otu49	1.000000	0.000000
+Otu87	Otu50	1.000000	0.000000
+Otu87	Otu51	1.000000	0.000000
+Otu87	Otu52	1.000000	0.000000
+Otu87	Otu53	1.000000	0.000000
+Otu87	Otu54	1.000000	0.000000
+Otu87	Otu55	1.000000	0.000000
+Otu87	Otu56	1.000000	0.000000
+Otu87	Otu57	1.000000	0.000000
+Otu87	Otu58	1.000000	0.000000
+Otu87	Otu59	1.000000	0.000000
+Otu87	Otu60	1.000000	0.000000
+Otu87	Otu61	1.000000	0.000000
+Otu87	Otu62	1.000000	0.000000
+Otu87	Otu63	1.000000	0.000000
+Otu87	Otu64	1.000000	0.000000
+Otu87	Otu65	1.000000	0.000000
+Otu87	Otu66	1.000000	0.000000
+Otu87	Otu67	1.000000	0.000000
+Otu87	Otu68	1.000000	0.000000
+Otu87	Otu69	1.000000	0.000000
+Otu87	Otu70	1.000000	0.000000
+Otu87	Otu71	1.000000	0.000000
+Otu87	Otu72	1.000000	0.000000
+Otu87	Otu73	1.000000	0.000000
+Otu87	Otu74	1.000000	0.000000
+Otu87	Otu75	1.000000	0.000000
+Otu87	Otu76	1.000000	0.000000
+Otu87	Otu77	1.000000	0.000000
+Otu87	Otu78	1.000000	0.000000
+Otu87	Otu79	1.000000	0.000000
+Otu87	Otu80	1.000000	0.000000
+Otu87	Otu81	1.000000	0.000000
+Otu87	Otu82	1.000000	0.000000
+Otu87	Otu83	1.000000	0.000000
+Otu87	Otu84	1.000000	0.000000
+Otu87	Otu85	1.000000	0.000000
+Otu87	Otu86	1.000000	0.000000
+Otu88	Otu01	-1.000000	0.000000
+Otu88	Otu02	1.000000	0.000000
+Otu88	Otu03	-1.000000	0.000000
+Otu88	Otu04	1.000000	0.000000
+Otu88	Otu05	-nan	0.000000
+Otu88	Otu06	-1.000000	0.000000
+Otu88	Otu07	-1.000000	0.000000
+Otu88	Otu08	-1.000000	0.000000
+Otu88	Otu09	-1.000000	0.000000
+Otu88	Otu10	-1.000000	0.000000
+Otu88	Otu11	-1.000000	0.000000
+Otu88	Otu12	-1.000000	0.000000
+Otu88	Otu13	-1.000000	0.000000
+Otu88	Otu14	-1.000000	0.000000
+Otu88	Otu15	-1.000000	0.000000
+Otu88	Otu16	-1.000000	0.000000
+Otu88	Otu17	-1.000000	0.000000
+Otu88	Otu18	-1.000000	0.000000
+Otu88	Otu19	-1.000000	0.000000
+Otu88	Otu20	-1.000000	0.000000
+Otu88	Otu21	-1.000000	0.000000
+Otu88	Otu22	-1.000000	0.000000
+Otu88	Otu23	-1.000000	0.000000
+Otu88	Otu24	1.000000	0.000000
+Otu88	Otu25	-1.000000	0.000000
+Otu88	Otu26	-1.000000	0.000000
+Otu88	Otu27	-1.000000	0.000000
+Otu88	Otu28	-1.000000	0.000000
+Otu88	Otu29	-1.000000	0.000000
+Otu88	Otu30	-1.000000	0.000000
+Otu88	Otu31	-1.000000	0.000000
+Otu88	Otu32	-1.000000	0.000000
+Otu88	Otu33	-1.000000	0.000000
+Otu88	Otu34	-1.000000	0.000000
+Otu88	Otu35	-1.000000	0.000000
+Otu88	Otu36	-1.000000	0.000000
+Otu88	Otu37	-1.000000	0.000000
+Otu88	Otu38	-1.000000	0.000000
+Otu88	Otu39	-1.000000	0.000000
+Otu88	Otu40	-1.000000	0.000000
+Otu88	Otu41	-1.000000	0.000000
+Otu88	Otu42	-1.000000	0.000000
+Otu88	Otu43	-1.000000	0.000000
+Otu88	Otu44	-1.000000	0.000000
+Otu88	Otu45	-1.000000	0.000000
+Otu88	Otu46	-1.000000	0.000000
+Otu88	Otu47	1.000000	0.000000
+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 22:08:08 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 22:08:08 2018 -0400
@@ -0,0 +1,12 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samplebiom.biom1	Tue Mar 20 22:08:08 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":[
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