changeset 2:54897b7e0551 draft default tip

Updated tool

--- a/phyloseq_filter.xml	Mon Nov 12 22:42:14 2018 -0500
+++ b/phyloseq_filter.xml	Thu Nov 22 08:13:52 2018 -0500
@@ -54,8 +54,8 @@
             <option value="Species">Species</option>
         </param>
         <param name="keep" size="10" type="integer" value="5" label="Number of the most abundant taxonomic rank units to keep in the filtered BIOM file" help="e.g. Phyla, Class and etc. as specified above. Select a value > 1."/>
-        <param name="cutoff" size="10" type="integer" value="5" label="Filter out OTUs. Remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples. Specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/>
-        <param name="nsample" size="10" type="float" value="0.5" label="Specify value of Y (where 1.0 = 100%)"/>
+        <param name="cutoff" size="10" type="integer" value="1" label="Filter out OTUs. Remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples. Specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/>
+        <param name="nsample" size="10" type="float" value="0.0" label="Specify value of Y (where 1.0 = 100%)"/>
     </inputs>
 
     <outputs>
@@ -70,11 +70,11 @@
                 <param name="input" value="GP.biom" ftype="biom1"/>
             </conditional>
             <output name="htmlfile" ftype="html" file="biom_out.html" />
-            <output name="outputbiom" file="out.biom" lines_diff="2" ftype="biom1"/>
-                <!-- <assert_contents>
+            <output name="outputbiom" >
+                <assert_contents>
                     <has_text text="Biological Observation Matrix"/>
                 </assert_contents>
-            </output> -->
+            </output>
         </test>
         <test>  <!-- Test #2: Test TABULAR format inputs -->
             <conditional name="file_source">

--- a/test-data/matrix_out.biom	Mon Nov 12 22:42:14 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-{"id":{},"format":"Biological Observation Matrix 1.0.0-dev","format_url":"http://biom-format.org/documentation/format_versions/biom-1.0.html","type":"OTU table","generated_by":"metagenomeSeq 1.20.0","date":"2018-11-13 02:21:49","matrix_type":"dense","matrix_element_type":"int","shape":[204,26],"rows":[{"id":"12812","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","koll13"]}},{"id":"546222","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales"]}},{"id":"313857","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":"252398","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":"331093","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":"317658","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":"329744","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","ACK-M1"]}},{"id":"242450","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales"]}},{"id":"556066","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Microbacteriaceae","Agromyces"]}},{"id":"543491","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia"]}},{"id":"58301","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia","Rothiaaeria"]}},{"id":"471141","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Micrococcaceae","Rothia","Rothiamucilaginosa"]}},{"id":"13034","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Actinomycetales","Mycobacteriaceae","Mycobacterium"]}},{"id":"469868","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumdentium"]}},{"id":"326977","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumadolescentis"]}},{"id":"469873","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium","Bifidobacteriumpseudocatenulatum"]}},{"id":"471180","metadata":{"taxonomy":["Bacteria","Actinobacteria","Actinobacteria","Bifidobacteriales","Bifidobacteriaceae","Bifidobacterium"]}},{"id":"60254","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Streptophyta"]}},{"id":"589787","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Streptophyta"]}},{"id":"535929","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Cryptophyta"]}},{"id":"308887","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"278521","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"561077","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"542011","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"332808","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"317182","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"549656","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"327536","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"340216","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Chloroplast","Stramenopiles"]}},{"id":"279599","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Nostocophycideae","Nostocales","Nostocaceae","Dolichospermum"]}},{"id":"235567","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Nostocophycideae","Nostocales","Nostocaceae"]}},{"id":"557211","metadata":{"taxonomy":["Bacteria","Cyanobacteria","Synechococcophycideae","Synechococcales","Synechococcaceae","Prochlorococcus"]}},{"id":"263681","metadata":{"taxonomy":["Bacteria","Cyanobacteria","4C0d-2","YS2"]}},{"id":"162077","metadata":{"taxonomy":["Bacteria","Proteobacteria","Epsilonproteobacteria","Campylobacterales","Campylobacteraceae","Campylobacter","Campylobacterconcisus"]}},{"id":"361480","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Alcaligenaceae"]}},{"id":"228077","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria"]}},{"id":"540352","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Neisseriales","Neisseriaceae"]}},{"id":"360229","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Neisseriales","Neisseriaceae","Neisseria"]}},{"id":"536311","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Neisseriales","Neisseriaceae","Kingella"]}},{"id":"551424","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria"]}},{"id":"279993","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria"]}},{"id":"165384","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria"]}},{"id":"114612","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Methylophilales","Methylophilaceae","Methylotenera"]}},{"id":"250544","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Methylophilales","Methylophilaceae","Methylotenera"]}},{"id":"107387","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Methylophilales","Methylophilaceae"]}},{"id":"156101","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Rhodocyclales"]}},{"id":"251263","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Oxalobacteraceae"]}},{"id":"324539","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Burkholderiaceae","Polynucleobacter"]}},{"id":"64871","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae","Hylemonella"]}},{"id":"141709","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae","Acidovorax"]}},{"id":"64550","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae","Acidovorax"]}},{"id":"592118","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae","Acidovorax","Acidovoraxdelafieldii"]}},{"id":"582407","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae","Limnohabitans"]}},{"id":"229790","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae"]}},{"id":"213853","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae"]}},{"id":"544356","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae"]}},{"id":"100099","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales","Comamonadaceae"]}},{"id":"101552","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales"]}},{"id":"342757","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales"]}},{"id":"200741","metadata":{"taxonomy":["Bacteria","Proteobacteria","Betaproteobacteria","Burkholderiales"]}},{"id":"9514","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Pasteurellales","Pasteurellaceae","Actinobacillus","Actinobacillusporcinus"]}},{"id":"94166","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Pasteurellales","Pasteurellaceae","Haemophilus","Haemophilusparainfluenzae"]}},{"id":"82772","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae","Morganella"]}},{"id":"550960","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae","Providencia"]}},{"id":"236788","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae","Edwardsiella","Edwardsiellaictaluri"]}},{"id":"262838","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae","Serratia","Serratiamarcescens"]}},{"id":"248470","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae"]}},{"id":"292134","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae"]}},{"id":"202356","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae"]}},{"id":"592346","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae","Klebsiella"]}},{"id":"557905","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Enterobacteriales","Enterobacteriaceae","Pantoea"]}},{"id":"484436","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Pseudomonadales","Moraxellaceae"]}},{"id":"346926","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Pseudomonadales","Moraxellaceae","Acinetobacter"]}},{"id":"107242","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Oceanospirillales","SUP05"]}},{"id":"593801","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Oceanospirillales","Halomonadaceae","CandidatusPortiera"]}},{"id":"323845","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Oceanospirillales","Halomonadaceae","CandidatusPortiera"]}},{"id":"338117","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Oceanospirillales","OM60"]}},{"id":"139864","metadata":{"taxonomy":["Bacteria","Proteobacteria","Gammaproteobacteria","Oceanospirillales","OM60"]}},{"id":"126508","meta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","Bacteroidetes","Bacteroidia","Bacteroidales"]}},{"id":"322235","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides","Bacteroidesuniformis"]}},{"id":"469778","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides","Bacteroidescoprophilus"]}},{"id":"158660","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides"]}},{"id":"331820","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides"]}},{"id":"244304","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides"]}},{"id":"315575","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides","Bacteroidescoprocola"]}},{"id":"130228","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides","Bacteroidesplebeius"]}},{"id":"560836","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Prevotellaceae","Prevotella"]}},{"id":"313753","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Prevotellaceae","Prevotella"]}},{"id":"198806","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Prevotellaceae","Prevotella"]}},{"id":"471122","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Prevotellaceae","Prevotella","Prevotellamelaninogenica"]}},{"id":"332311","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides","Bacteroideseggerthii"]}},{"id":"361496","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides"]}},{"id":"127309","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides"]}},{"id":"248140","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides","Bacteroidescaccae"]}},{"id":"348374","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Bacteroidaceae","Bacteroides"]}},{"id":"291090","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Porphyromonadaceae","Parabacteroides","Parabacteroidesdistasonis"]}},{"id":"470761","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Porphyromonadaceae","Parabacteroides","Parabacteroidesjohnsonii"]}},{"id":"259569","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Rikenellaceae","Alistipes","Alistipesputredinis"]}},{"id":"104780","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Rikenellaceae","Alistipes"]}},{"id":"181095","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Bacteroidia","Bacteroidales","Rikenellaceae","Alistipes"]}},{"id":"415279","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Sphingobacteria","Sphingobacteriales"]}},{"id":"574458","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Sphingobacteria","Sphingobacteriales"]}},{"id":"235904","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Sphingobacteria","Sphingobacteriales"]}},{"id":"113307","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Sphingobacteria","Sphingobacteriales"]}},{"id":"127471","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Sphingobacteria","Sphingobacteriales"]}},{"id":"558023","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Sphingobacteria","Sphingobacteriales"]}},{"id":"241123","metadata":{"taxonomy":["Bacteria","Bacteroidetes","Sphingobacteria","Sphingobacteriales"]}},{"id":"203996","metadata":{"taxonomy":["Bacteria","Proteobacteria","Deltaproteobacteria","Desulfobacterales"]}},{"id":"325608","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales"]}},{"id":"510994","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales"]}},{"id":"298875","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Clostridiaceae","Clostridium"]}},{"id":"359171","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","ClostridialesFamilyXI.IncertaeSedis","Anaerococcus","Anaerococcushydrogenalis"]}},{"id":"469661","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Eubacteriaceae","Anaerofustis","Anaerofustisstercorihominis"]}},{"id":"267192","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Clostridiaceae","Clostridium"]}},{"id":"346780","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Clostridiaceae","Clostridium"]}},{"id":"579564","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Clostridiaceae","Clostridium"]}},{"id":"165334","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Catabacteriaceae"]}},{"id":"192573","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae"]}},{"id":"287978","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae"]}},{"id":"318444","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Blautia","Blautiaproducta"]}},{"id":"199487","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Blautia"]}},{"id":"299892","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Blautia"]}},{"id":"192127","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae"]}},{"id":"469890","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae"]}},{"id":"194053","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Roseburia"]}},{"id":"518438","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Roseburia"]}},{"id":"357795","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Roseburia","Eubacteriumrectale"]}},{"id":"352304","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae"]}},{"id":"545473","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Clostridium"]}},{"id":"470747","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Oribacterium","Oribacteriumsinus"]}},{"id":"288134","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae"]}},{"id":"190464","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae"]}},{"id":"360796","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Dorea"]}},{"id":"261912","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Dorea","Doreaformicigenerans"]}},{"id":"193876","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Ruminococcus"]}},{"id":"294022","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Ruminococcus"]}},{"id":"511008","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Ruminococcus"]}},{"id":"470973","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Ruminococcus","Ruminococcustorques"]}},{"id":"162162","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Ruminococcus"]}},{"id":"262724","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae"]}},{"id":"316732","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae","Lachnospira"]}},{"id":"196731","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Lachnospiraceae"]}},{"id":"365676","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae","Ruminococcus"]}},{"id":"187524","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae"]}},{"id":"191541","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae"]}},{"id":"212619","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae"]}},{"id":"471106","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae"]}},{"id":"357470","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae","Faecalibacterium"]}},{"id":"325407","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae","Faecalibacterium"]}},{"id":"171551","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae","Faecalibacterium","Faecalibacteriumprausnitzii"]}},{"id":"290260","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae","Faecalibacterium","Faecalibacteriumprausnitzii"]}},{"id":"367433","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae","Faecalibacterium","Faecalibacteriumprausnitzii"]}},{"id":"193761","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae","Faecalibacterium"]}},{"id":"327476","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae","Faecalibacterium"]}},{"id":"189047","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae"]}},{"id":"180658","metadata":{"taxonomy":["Bacteria","Firmicutes","Clostridia","Clostridiales","Ruminococcaceae"]}},{"id":"269833","met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\ No newline at end of file

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--- a/test-data/out.biom	Mon Nov 12 22:42:14 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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South Carolina Pine soil, pH 4.9"}},{"id":"CC1","metadata":{"X.SampleID":"CC1","Primer":"ILBC_02","Final_Barcode":"AACTCG","Barcode_truncated_plus_T":"CGAGTT","Barcode_full_length":"CATCGACGAGT","SampleType":"Soil","Description":"Cedar Creek Minnesota, grassland, pH 6.1"}},{"id":"SV1","metadata":{"X.SampleID":"SV1","Primer":"ILBC_03","Final_Barcode":"AACTGT","Barcode_truncated_plus_T":"ACAGTT","Barcode_full_length":"GTACGCACAGT","SampleType":"Soil","Description":"Sevilleta new Mexico, desert scrub, pH 8.3"}},{"id":"M31Fcsw","metadata":{"X.SampleID":"M31Fcsw","Primer":"ILBC_04","Final_Barcode":"AAGAGA","Barcode_truncated_plus_T":"TCTCTT","Barcode_full_length":"TCGACATCTCT","SampleType":"Feces","Description":"M3, Day 1, fecal swab, whole body study"}},{"id":"M11Fcsw","metadata":{"X.SampleID":"M11Fcsw","Primer":"ILBC_05","Final_Barcode":"AAGCTG","Barcode_truncated_plus_T":"CAGCTT","Barcode_full_length":"CGACTGCAGCT","SampleType":"Feces","Description":"M1, Day 1, fecal swab, whole body study "}},{"id":"M31Plmr","metadata":{"X.SampleID":"M31Plmr","Primer":"ILBC_07","Final_Barcode":"AATCGT","Barcode_truncated_plus_T":"ACGATT","Barcode_full_length":"CGAGTCACGAT","SampleType":"Skin","Description":"M3, Day 1, right palm, whole body study"}},{"id":"M11Plmr","metadata":{"X.SampleID":"M11Plmr","Primer":"ILBC_08","Final_Barcode":"ACACAC","Barcode_truncated_plus_T":"GTGTGT","Barcode_full_length":"GCCATAGTGTG","SampleType":"Skin","Description":"M1, Day 1, right palm, whole body study "}},{"id":"F21Plmr","metadata":{"X.SampleID":"F21Plmr","Primer":"ILBC_09","Final_Barcode":"ACACAT","Barcode_truncated_plus_T":"ATGTGT","Barcode_full_length":"GTAGACATGTG","SampleType":"Skin","Description":"F1, Day 1,  right palm, whole body study "}},{"id":"M31Tong","metadata":{"X.SampleID":"M31Tong","Primer":"ILBC_10","Final_Barcode":"ACACGA","Barcode_truncated_plus_T":"TCGTGT","Barcode_full_length":"TGTGGCTCGTG","SampleType":"Tongue","Description":"M3, Day 1, tongue, whole body study "}},{"id":"M11Tong","metadata":{"X.SampleID":"M11Tong","Primer":"ILBC_11","Final_Barcode":"ACACGG","Barcode_truncated_plus_T":"CCGTGT","Barcode_full_length":"TAGACACCGTG","SampleType":"Tongue","Description":"M1, Day 1, tongue, whole body study "}},{"id":"LMEpi24M","metadata":{"X.SampleID":"LMEpi24M","Primer":"ILBC_13","Final_Barcode":"ACACTG","Barcode_truncated_plus_T":"CAGTGT","Barcode_full_length":"CATGAACAGTG","SampleType":"Freshwater","Description":"Lake Mendota Minnesota, 24 meter epilimnion "}},{"id":"SLEpi20M","metadata":{"X.SampleID":"SLEpi20M","Primer":"ILBC_15","Final_Barcode":"ACAGAG","Barcode_truncated_plus_T":"CTCTGT","Barcode_full_length":"AGCCGACTCTG","SampleType":"Freshwater","Description":"Sparkling Lake Wisconsin, 20 meter eplimnion"}},{"id":"AQC1cm","metadata":{"X.SampleID":"AQC1cm","Primer":"ILBC_16","Final_Barcode":"ACAGCA","Barcode_truncated_plus_T":"TGCTGT","Barcode_full_length":"GACCACTGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 0-1cm depth"}},{"id":"AQC4cm","metadata":{"X.SampleID":"AQC4cm","Primer":"ILBC_17","Final_Barcode":"ACAGCT","Barcode_truncated_plus_T":"AGCTGT","Barcode_full_length":"CAAGCTAGCTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 3-4 cm depth"}},{"id":"AQC7cm","metadata":{"X.SampleID":"AQC7cm","Primer":"ILBC_18","Final_Barcode":"ACAGTG","Barcode_truncated_plus_T":"CACTGT","Barcode_full_length":"ATGAAGCACTG","SampleType":"Freshwater (creek)","Description":"Allequash Creek, 6-7 cm depth"}},{"id":"NP2","metadata":{"X.SampleID":"NP2","Primer":"ILBC_19","Final_Barcode":"ACAGTT","Barcode_truncated_plus_T":"AACTGT","Barcode_full_length":"TCGCGCAACTG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 1"}},{"id":"NP3","metadata":{"X.SampleID":"NP3","Primer":"ILBC_20","Final_Barcode":"ACATCA","Barcode_truncated_plus_T":"TGATGT","Barcode_full_length":"GCTAAGTGATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 2"}},{"id":"NP5","metadata":{"X.SampleID":"NP5","Primer":"ILBC_21","Final_Barcode":"ACATGA","Barcode_truncated_plus_T":"TCATGT","Barcode_full_length":"GAACGATCATG","SampleType":"Ocean","Description":"Newport Pier, CA surface water, Time 3"}},{"id":"TRRsed1","metadata":{"X.SampleID":"TRRsed1","Primer":"ILBC_22","Final_Barcode":"ACATGT","Barcode_truncated_plus_T":"ACATGT","Barcode_full_length":"CACGTGACATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 1"}},{"id":"TRRsed2","metadata":{"X.SampleID":"TRRsed2","Primer":"ILBC_23","Final_Barcode":"ACATTC","Barcode_truncated_plus_T":"GAATGT","Barcode_full_length":"TGCGCTGAATG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 2"}},{"id":"TRRsed3","metadata":{"X.SampleID":"TRRsed3","Primer":"ILBC_24","Final_Barcode":"ACCACA","Barcode_truncated_plus_T":"TGTGGT","Barcode_full_length":"GATGTATGTGG","SampleType":"Sediment (estuary)","Description":"Tijuana River Reserve, depth 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