| Previous changeset 1:06c8f1be0f31 (2017-09-05) Next changeset 3:5d472f04851b (2018-04-06) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3 |
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modified:
macros.xml tree.shared.xml |
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added:
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 |
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| diff -r 06c8f1be0f31 -r 506ad7182cfb macros.xml --- a/macros.xml Tue Sep 05 16:53:53 2017 -0400 +++ b/macros.xml Tue Mar 20 22:19:37 2018 -0400 |
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| b'@@ -1,11 +1,13 @@\n <macros>\n+ <token name="@WRAPPER_VERSION@">1.39.5</token>\n <xml name="requirements">\n <requirements>\n- <requirement type="package" version="1.36.1">mothur</requirement>\n+ <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>\n+ <yield/>\n </requirements>\n </xml>\n <xml name="version_command">\n- <version_command>mothur "#help()" | sed \'7q;d\' | cut -d" " -f2 </version_command>\n+ <version_command><![CDATA[ mothur "#help()" | sed \'7q;d\' | cut -d" " -f2 ]]></version_command>\n </xml>\n <xml name="stdio">\n <stdio>\n@@ -13,20 +15,10 @@\n <exit_code range="1:" level="fatal"/>\n </stdio>\n </xml>\n- <token name="@WRAPPER_VERSION@">1.36.1</token>\n <token name="@SHELL_OPTIONS@">set -o pipefail;</token>\n- <token name="@MOTHUR_OVERVIEW@">\n-<![CDATA[\n-\n-**Mothur Overview**\n \n-Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team\n-in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.\n \n-.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page\n-\n-]]>\n- </token>\n+ <!-- Input parameters -->\n <xml name="labeloptions">\n <options>\n <filter type="data_meta" ref="otu" key="labels"/>\n@@ -78,9 +70,70 @@\n <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>\n <yield/>\n </xml>\n+\n+ <!-- CLUSTERING -->\n+ <xml name="param-clustermethods">\n+ <param argument="method" type="select" label="Clustering Method">\n+ <option value="opti" selected="true">Opticlust method</option>\n+ <option value="furthest">Furthest neighbor</option>\n+ <option value="nearest">Nearest neighbor</option>\n+ <option value="average">Average neighbor</option>\n+ <yield/>\n+ </param>\n+ </xml>\n+ <xml name="option-vsearch-clustermethods">\n+ <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option>\n+ <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option>\n+ </xml>\n+ <xml name="params-opticlust">\n+ <param argument="metric" type="select" label="metric - select the metric in the opticluster method"\n+ help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn),\n+ false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score),\n+ accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.">\n+ <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option>\n+ <option value="sens">Sensitivity</option>\n+ <option value="spec">specificity</option>\n+ <option value="tptn">true positives + true negatives</option>\n+ <option value="fpfn">false positives + false negatives</option>\n+ <option value="tp">true positives</option>\n+ <option value="tn">true negative</option>\n+ <option value="fp">false positive</option>\n+ <option value="fn">false negative</option>\n+ <option value="f1score">f1score</option>\n+ <option value="accuracy">accuracy</option>\n+ <option value="ppv">positive predictive value</option>\n+ <option value="npv">negative predictive value</option>\n+ <option value="fdr">false discovery rate</option>\n+ </param>\n+ <param argument="initialize" type="select" label="Initial randomization"\n+ help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one'..b'ng expression="^name\\tpound\\tdash\\tplus\\tequal\\tloop\\ttilde\\ttotal\\tnumseqs$"/>\n+ </xml>\n+ <xml name="test-alignreport-format">\n+ <has_line_matching expression="^QueryName\\tQueryLength\\tTemplateName\\tTemplateLength\\tSearchMethod\\tSearchScore\\tAlignmentMethod\\tQueryStart\\tQueryEnd\\tTemplateStart\\tTemplateEnd\\tPairwiseAlignmentLength\\tGapsInQuery\\tGapsInTemplate\\tLongestInsert\\tSimBtwnQuery&Template$"/>\n+ </xml>\n+ <xml name="test-axes-format">\n+ <has_line_matching expression="^group(\\taxis\\d+)+$"/>\n+ </xml>\n+ <xml name="test-chimera-format">\n+ <has_line_matching expression="Score\\tQuery\\tParentA\\tParentB\\tIdQM\\tIdQA\\tIdQB\\tIdAB\\tIdQT\\tLY\\tLN\\tLA\\tRY\\tRN\\tRA\\tDiv\\tYN"/>\n+ </xml>\n+ <xml name="test-column-format">\n+ <has_n_columns n="3"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+\\t[\\w\\d\\-]+\\t[\\d\\.]+$"/>\n+ </xml>\n+ <xml name="test-contigsreport-format">\n+ <has_n_columns n="7"/>\n+ <has_line_matching expression="^Name\\tLength\\tOverlap_Length\\tOverlap_Start\\tOverlap_End\\tMisMatches\\tNum_Ns$"/>\n+ </xml>\n+ <xml name="test-count-format">\n+ <has_line_matching expression="^Representative_Sequence\\ttotal(\\t\\w+)*$"/>\n+ <has_line_matching expression="^\\w+(\\t\\d+)+(\\s)*$"/>\n+ </xml>\n+ <xml name="test-dist-format">\n+ <has_line_matching expression="^[ \\t]*\\d+$"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+(\\t[\\d\\.]+)+\\s?$"/>\n+ </xml>\n+ <xml name="test-fasta-format">\n+ <has_line_matching expression="^>.+$"/>\n+ <has_line_matching expression="^[ACTGN-]+$"/>\n+ </xml>\n+ <xml name="test-fastq-format">\n+ <has_line_matching expression="^@.+$"/>\n+ <has_line_matching expression="^[ACTGN]+$"/>\n+ <has_line_matching expression="^\\+$"/>\n+ </xml>\n+ <xml name="test-group-format">\n+ <has_line_matching expression="^Representative_Sequence\\ttotal(\\t[\\w\\d\\-]+)+$"/>\n+ <has_line_matching expression="^[\\w\\d\\-]+(\\t\\d+)+$"/>\n+ </xml>\n+ <xml name="test-list-format">\n+ <has_line_matching expression="^label\\tnumOtus(\\tOtu\\d+)+$"/>\n+ <has_line_matching expression="^(unique|0\\.\\d+)\\t\\d+(\\t[\\w\\d\\-,]+)+$"/>\n+ </xml>\n+ <xml name="test-names-format">\n+ <has_line_matching expression="^[a-zA-Z0-9]+\\t[a-zA-Z0-9]+$"/>\n+ </xml>\n+ <xml name="test-qfile-format">\n+ <has_line_matching expression="^(\\d+ )+$"/>\n+ <has_line_matching expression="^>.+$"/>\n+ </xml>\n+ <xml name="test-rabund-format">\n+ <has_line_matching expression="^(unique|0\\.\\d+)(\\t\\d+\\.?\\d*)+$"/>\n+ </xml>\n+ <xml name="test-sabund-format">\n+ <has_line_matching expression="^(unique|0\\.\\d+)(\\t\\d+)+$"/>\n+ </xml>\n+ <xml name="test-sensspec-format">\n+ <has_n_columns n="14"/>\n+ <has_line_matching expression="^label\\tcutoff\\ttp\\ttn\\tfp\\tfn\\tsensitivity\\tspecificity\\tppv\\tnpv\\tfdr\\taccuracy\\t\\w+\\tf1score$"/>\n+ </xml>\n+ <xml name="test-shared-format">\n+ <has_line_matching expression="^label\\tGroup\\tnumOtus(\\t(Otu|rareOTUs|.*OTU.*)\\d+)+$"/>\n+ </xml>\n+ <xml name="test-taxonomy-format">\n+ <has_n_columns n="3"/>\n+ <has_line_matching expression="^OTU\\tSize\\tTaxonomy$"/>\n+ </xml>\n+ <xml name="test-taxsummary-format">\n+ <has_line_matching expression="^((taxlevel\\trankID\\ttaxon\\tdaughterlevels\\ttotal(\\t[\\w\\d\\-]+)*)|(taxonomy\\ttotal(\\t[\\w\\d]+)*))$"/>\n+ </xml>\n+ <!-- backmatter -->\n+ <token name="@MOTHUR_OVERVIEW@">\n+<![CDATA[\n+\n+**Mothur Overview**\n+\n+Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team\n+in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.\n+\n+.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page\n+\n+]]>\n+ </token>\n <xml name="citations">\n <citations>\n <citation type="doi">10.1128/AEM.01541-09</citation>\n' |
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| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/Fasting_Example1.scrap.sff |
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| Binary file test-data/Fasting_Example1.scrap.sff has changed |
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| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/amazon.an.0.03.pearson.otu.corr --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.an.0.03.pearson.otu.corr Tue Mar 20 22:19:37 2018 -0400 |
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| b'@@ -0,0 +1,3829 @@\n+OTUA\tOTUB\tpearsonCoef\tSignificance\n+Otu02\tOtu01\t-1.000000\t0.000000\n+Otu03\tOtu01\t1.000000\t0.000000\n+Otu03\tOtu02\t-1.000000\t0.000000\n+Otu04\tOtu01\t-1.000000\t0.000000\n+Otu04\tOtu02\t1.000000\t0.000000\n+Otu04\tOtu03\t-1.000000\t0.000000\n+Otu05\tOtu01\t-nan\t0.000000\n+Otu05\tOtu02\t-nan\t0.000000\n+Otu05\tOtu03\t-nan\t0.000000\n+Otu05\tOtu04\t-nan\t0.000000\n+Otu06\tOtu01\t1.000000\t0.000000\n+Otu06\tOtu02\t-1.000000\t0.000000\n+Otu06\tOtu03\t1.000000\t0.000000\n+Otu06\tOtu04\t-1.000000\t0.000000\n+Otu06\tOtu05\t-nan\t0.000000\n+Otu07\tOtu01\t1.000000\t0.000000\n+Otu07\tOtu02\t-1.000000\t0.000000\n+Otu07\tOtu03\t1.000000\t0.000000\n+Otu07\tOtu04\t-1.000000\t0.000000\n+Otu07\tOtu05\t-nan\t0.000000\n+Otu07\tOtu06\t1.000000\t0.000000\n+Otu08\tOtu01\t1.000000\t0.000000\n+Otu08\tOtu02\t-1.000000\t0.000000\n+Otu08\tOtu03\t1.000000\t0.000000\n+Otu08\tOtu04\t-1.000000\t0.000000\n+Otu08\tOtu05\t-nan\t0.000000\n+Otu08\tOtu06\t1.000000\t0.000000\n+Otu08\tOtu07\t1.000000\t0.000000\n+Otu09\tOtu01\t1.000000\t0.000000\n+Otu09\tOtu02\t-1.000000\t0.000000\n+Otu09\tOtu03\t1.000000\t0.000000\n+Otu09\tOtu04\t-1.000000\t0.000000\n+Otu09\tOtu05\t-nan\t0.000000\n+Otu09\tOtu06\t1.000000\t0.000000\n+Otu09\tOtu07\t1.000000\t0.000000\n+Otu09\tOtu08\t1.000000\t0.000000\n+Otu10\tOtu01\t1.000000\t0.000000\n+Otu10\tOtu02\t-1.000000\t0.000000\n+Otu10\tOtu03\t1.000000\t0.000000\n+Otu10\tOtu04\t-1.000000\t0.000000\n+Otu10\tOtu05\t-nan\t0.000000\n+Otu10\tOtu06\t1.000000\t0.000000\n+Otu10\tOtu07\t1.000000\t0.000000\n+Otu10\tOtu08\t1.000000\t0.000000\n+Otu10\tOtu09\t1.000000\t0.000000\n+Otu11\tOtu01\t1.000000\t0.000000\n+Otu11\tOtu02\t-1.000000\t0.000000\n+Otu11\tOtu03\t1.000000\t0.000000\n+Otu11\tOtu04\t-1.000000\t0.000000\n+Otu11\tOtu05\t-nan\t0.000000\n+Otu11\tOtu06\t1.000000\t0.000000\n+Otu11\tOtu07\t1.000000\t0.000000\n+Otu11\tOtu08\t1.000000\t0.000000\n+Otu11\tOtu09\t1.000000\t0.000000\n+Otu11\tOtu10\t1.000000\t0.000000\n+Otu12\tOtu01\t1.000000\t0.000000\n+Otu12\tOtu02\t-1.000000\t0.000000\n+Otu12\tOtu03\t1.000000\t0.000000\n+Otu12\tOtu04\t-1.000000\t0.000000\n+Otu12\tOtu05\t-nan\t0.000000\n+Otu12\tOtu06\t1.000000\t0.000000\n+Otu12\tOtu07\t1.000000\t0.000000\n+Otu12\tOtu08\t1.000000\t0.000000\n+Otu12\tOtu09\t1.000000\t0.000000\n+Otu12\tOtu10\t1.000000\t0.000000\n+Otu12\tOtu11\t1.000000\t0.000000\n+Otu13\tOtu01\t1.000000\t0.000000\n+Otu13\tOtu02\t-1.000000\t0.000000\n+Otu13\tOtu03\t1.000000\t0.000000\n+Otu13\tOtu04\t-1.000000\t0.000000\n+Otu13\tOtu05\t-nan\t0.000000\n+Otu13\tOtu06\t1.000000\t0.000000\n+Otu13\tOtu07\t1.000000\t0.000000\n+Otu13\tOtu08\t1.000000\t0.000000\n+Otu13\tOtu09\t1.000000\t0.000000\n+Otu13\tOtu10\t1.000000\t0.000000\n+Otu13\tOtu11\t1.000000\t0.000000\n+Otu13\tOtu12\t1.000000\t0.000000\n+Otu14\tOtu01\t1.000000\t0.000000\n+Otu14\tOtu02\t-1.000000\t0.000000\n+Otu14\tOtu03\t1.000000\t0.000000\n+Otu14\tOtu04\t-1.000000\t0.000000\n+Otu14\tOtu05\t-nan\t0.000000\n+Otu14\tOtu06\t1.000000\t0.000000\n+Otu14\tOtu07\t1.000000\t0.000000\n+Otu14\tOtu08\t1.000000\t0.000000\n+Otu14\tOtu09\t1.000000\t0.000000\n+Otu14\tOtu10\t1.000000\t0.000000\n+Otu14\tOtu11\t1.000000\t0.000000\n+Otu14\tOtu12\t1.000000\t0.000000\n+Otu14\tOtu13\t1.000000\t0.000000\n+Otu15\tOtu01\t1.000000\t0.000000\n+Otu15\tOtu02\t-1.000000\t0.000000\n+Otu15\tOtu03\t1.000000\t0.000000\n+Otu15\tOtu04\t-1.000000\t0.000000\n+Otu15\tOtu05\t-nan\t0.000000\n+Otu15\tOtu06\t1.000000\t0.000000\n+Otu15\tOtu07\t1.000000\t0.000000\n+Otu15\tOtu08\t1.000000\t0.000000\n+Otu15\tOtu09\t1.000000\t0.000000\n+Otu15\tOtu10\t1.000000\t0.000000\n+Otu15\tOtu11\t1.000000\t0.000000\n+Otu15\tOtu12\t1.000000\t0.000000\n+Otu15\tOtu13\t1.000000\t0.000000\n+Otu15\tOtu14\t1.000000\t0.000000\n+Otu16\tOtu01\t1.000000\t0.000000\n+Otu16\tOtu02\t-1.000000\t0.000000\n+Otu16\tOtu03\t1.000000\t0.000000\n+Otu16\tOtu04\t-1.000000\t0.000000\n+Otu16\tOtu05\t-nan\t0.000000\n+Otu16\tOtu06\t1.000000\t0.000000\n+Otu16\tOtu07\t1.000000\t0.000000\n+Otu16\tOtu08\t1.000000\t0.000000\n+Otu16\tOtu09\t1.000000\t0.000000\n+Otu16\tOtu10\t1.000000\t0.000000\n+Otu16\tOtu11\t1.000000\t0.000000\n+Otu16\tOtu12\t1.000000\t0.000000\n+Otu16\tOtu13\t1.000000\t0.000000\n+Otu16\tOtu14\t1.000000\t0.000000\n+Otu16\tOtu15\t1.000000\t0.000000\n+Otu17\tOtu01\t1.000000\t0.000000\n+Otu17\tOtu02\t-1.000000\t0.000000\n+Otu17\tOtu03\t1.000000\t0.000000\n+Otu17\tOtu04\t-1.000000\t0.000000\n+Otu17\tOtu05\t-nan\t0.000000\n+Otu17\tOtu06\t1.000000\t0.000000\n+Otu17\tOtu07\t1.000000\t0.000000\n+Otu17\tOtu08\t1.000000\t0.000000\n+Otu17\tOtu09'..b'tu46\t-1.000000\t0.000000\n+Otu87\tOtu47\t1.000000\t0.000000\n+Otu87\tOtu48\t1.000000\t0.000000\n+Otu87\tOtu49\t1.000000\t0.000000\n+Otu87\tOtu50\t1.000000\t0.000000\n+Otu87\tOtu51\t1.000000\t0.000000\n+Otu87\tOtu52\t1.000000\t0.000000\n+Otu87\tOtu53\t1.000000\t0.000000\n+Otu87\tOtu54\t1.000000\t0.000000\n+Otu87\tOtu55\t1.000000\t0.000000\n+Otu87\tOtu56\t1.000000\t0.000000\n+Otu87\tOtu57\t1.000000\t0.000000\n+Otu87\tOtu58\t1.000000\t0.000000\n+Otu87\tOtu59\t1.000000\t0.000000\n+Otu87\tOtu60\t1.000000\t0.000000\n+Otu87\tOtu61\t1.000000\t0.000000\n+Otu87\tOtu62\t1.000000\t0.000000\n+Otu87\tOtu63\t1.000000\t0.000000\n+Otu87\tOtu64\t1.000000\t0.000000\n+Otu87\tOtu65\t1.000000\t0.000000\n+Otu87\tOtu66\t1.000000\t0.000000\n+Otu87\tOtu67\t1.000000\t0.000000\n+Otu87\tOtu68\t1.000000\t0.000000\n+Otu87\tOtu69\t1.000000\t0.000000\n+Otu87\tOtu70\t1.000000\t0.000000\n+Otu87\tOtu71\t1.000000\t0.000000\n+Otu87\tOtu72\t1.000000\t0.000000\n+Otu87\tOtu73\t1.000000\t0.000000\n+Otu87\tOtu74\t1.000000\t0.000000\n+Otu87\tOtu75\t1.000000\t0.000000\n+Otu87\tOtu76\t1.000000\t0.000000\n+Otu87\tOtu77\t1.000000\t0.000000\n+Otu87\tOtu78\t1.000000\t0.000000\n+Otu87\tOtu79\t1.000000\t0.000000\n+Otu87\tOtu80\t1.000000\t0.000000\n+Otu87\tOtu81\t1.000000\t0.000000\n+Otu87\tOtu82\t1.000000\t0.000000\n+Otu87\tOtu83\t1.000000\t0.000000\n+Otu87\tOtu84\t1.000000\t0.000000\n+Otu87\tOtu85\t1.000000\t0.000000\n+Otu87\tOtu86\t1.000000\t0.000000\n+Otu88\tOtu01\t-1.000000\t0.000000\n+Otu88\tOtu02\t1.000000\t0.000000\n+Otu88\tOtu03\t-1.000000\t0.000000\n+Otu88\tOtu04\t1.000000\t0.000000\n+Otu88\tOtu05\t-nan\t0.000000\n+Otu88\tOtu06\t-1.000000\t0.000000\n+Otu88\tOtu07\t-1.000000\t0.000000\n+Otu88\tOtu08\t-1.000000\t0.000000\n+Otu88\tOtu09\t-1.000000\t0.000000\n+Otu88\tOtu10\t-1.000000\t0.000000\n+Otu88\tOtu11\t-1.000000\t0.000000\n+Otu88\tOtu12\t-1.000000\t0.000000\n+Otu88\tOtu13\t-1.000000\t0.000000\n+Otu88\tOtu14\t-1.000000\t0.000000\n+Otu88\tOtu15\t-1.000000\t0.000000\n+Otu88\tOtu16\t-1.000000\t0.000000\n+Otu88\tOtu17\t-1.000000\t0.000000\n+Otu88\tOtu18\t-1.000000\t0.000000\n+Otu88\tOtu19\t-1.000000\t0.000000\n+Otu88\tOtu20\t-1.000000\t0.000000\n+Otu88\tOtu21\t-1.000000\t0.000000\n+Otu88\tOtu22\t-1.000000\t0.000000\n+Otu88\tOtu23\t-1.000000\t0.000000\n+Otu88\tOtu24\t1.000000\t0.000000\n+Otu88\tOtu25\t-1.000000\t0.000000\n+Otu88\tOtu26\t-1.000000\t0.000000\n+Otu88\tOtu27\t-1.000000\t0.000000\n+Otu88\tOtu28\t-1.000000\t0.000000\n+Otu88\tOtu29\t-1.000000\t0.000000\n+Otu88\tOtu30\t-1.000000\t0.000000\n+Otu88\tOtu31\t-1.000000\t0.000000\n+Otu88\tOtu32\t-1.000000\t0.000000\n+Otu88\tOtu33\t-1.000000\t0.000000\n+Otu88\tOtu34\t-1.000000\t0.000000\n+Otu88\tOtu35\t-1.000000\t0.000000\n+Otu88\tOtu36\t-1.000000\t0.000000\n+Otu88\tOtu37\t-1.000000\t0.000000\n+Otu88\tOtu38\t-1.000000\t0.000000\n+Otu88\tOtu39\t-1.000000\t0.000000\n+Otu88\tOtu40\t-1.000000\t0.000000\n+Otu88\tOtu41\t-1.000000\t0.000000\n+Otu88\tOtu42\t-1.000000\t0.000000\n+Otu88\tOtu43\t-1.000000\t0.000000\n+Otu88\tOtu44\t-1.000000\t0.000000\n+Otu88\tOtu45\t-1.000000\t0.000000\n+Otu88\tOtu46\t-1.000000\t0.000000\n+Otu88\tOtu47\t1.000000\t0.000000\n+Otu88\tOtu48\t1.000000\t0.000000\n+Otu88\tOtu49\t1.000000\t0.000000\n+Otu88\tOtu50\t1.000000\t0.000000\n+Otu88\tOtu51\t1.000000\t0.000000\n+Otu88\tOtu52\t1.000000\t0.000000\n+Otu88\tOtu53\t1.000000\t0.000000\n+Otu88\tOtu54\t1.000000\t0.000000\n+Otu88\tOtu55\t1.000000\t0.000000\n+Otu88\tOtu56\t1.000000\t0.000000\n+Otu88\tOtu57\t1.000000\t0.000000\n+Otu88\tOtu58\t1.000000\t0.000000\n+Otu88\tOtu59\t1.000000\t0.000000\n+Otu88\tOtu60\t1.000000\t0.000000\n+Otu88\tOtu61\t1.000000\t0.000000\n+Otu88\tOtu62\t1.000000\t0.000000\n+Otu88\tOtu63\t1.000000\t0.000000\n+Otu88\tOtu64\t1.000000\t0.000000\n+Otu88\tOtu65\t1.000000\t0.000000\n+Otu88\tOtu66\t1.000000\t0.000000\n+Otu88\tOtu67\t1.000000\t0.000000\n+Otu88\tOtu68\t1.000000\t0.000000\n+Otu88\tOtu69\t1.000000\t0.000000\n+Otu88\tOtu70\t1.000000\t0.000000\n+Otu88\tOtu71\t1.000000\t0.000000\n+Otu88\tOtu72\t1.000000\t0.000000\n+Otu88\tOtu73\t1.000000\t0.000000\n+Otu88\tOtu74\t1.000000\t0.000000\n+Otu88\tOtu75\t1.000000\t0.000000\n+Otu88\tOtu76\t1.000000\t0.000000\n+Otu88\tOtu77\t1.000000\t0.000000\n+Otu88\tOtu78\t1.000000\t0.000000\n+Otu88\tOtu79\t1.000000\t0.000000\n+Otu88\tOtu80\t1.000000\t0.000000\n+Otu88\tOtu81\t1.000000\t0.000000\n+Otu88\tOtu82\t1.000000\t0.000000\n+Otu88\tOtu83\t1.000000\t0.000000\n+Otu88\tOtu84\t1.000000\t0.000000\n+Otu88\tOtu85\t1.000000\t0.000000\n+Otu88\tOtu86\t1.000000\t0.000000\n+Otu88\tOtu87\t1.000000\t0.000000\n' |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/amazon.otus.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/amazon.otus.accnos Tue Mar 20 22:19:37 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Otu01 +Otu17 +Otu42 |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/esophagus.fn.shared --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/esophagus.fn.shared Tue Mar 20 22:19:37 2018 -0400 |
| b |
| @@ -0,0 +1,12 @@ +unique B 593 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 3 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 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 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 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 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 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 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 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 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 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 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 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 +unique C 593 0 0 0 0 0 0 0 0 0 0 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 0 0 0 0 0 0 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 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 4 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 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 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 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 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 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +unique D 593 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 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 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 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 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 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 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 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 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 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 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 0 0 1 1 1 1 1 1 1 1 1 30 1 1 8 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +0.03 B 87 12 17 16 14 1 2 39 1 1 18 8 6 1 1 2 5 1 7 3 1 12 3 6 2 1 1 1 3 1 2 1 1 1 2 1 1 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 0 0 0 0 0 +0.03 C 87 0 0 19 42 0 0 6 2 10 19 7 1 0 0 2 0 5 0 3 2 0 4 2 0 0 0 1 0 0 0 2 0 2 14 0 0 0 7 0 0 0 0 0 29 14 4 2 2 3 2 11 1 3 3 1 8 6 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 0 0 +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 |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/samplebiom.biom1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samplebiom.biom1 Tue Mar 20 22:19:37 2018 -0400 |
| [ |
| b'@@ -0,0 +1,8668 @@\n+{\n+ "id":"otu.dat-0.03",\n+ "format": "Biological Observation Matrix 0.9.1",\n+ "format_url": "http://biom-format.org",\n+ "type": "OTU table",\n+ "generated_by": "mothur1.36.1",\n+ "date": "Mon Jun 26 15:11:52 2017",\n+ "rows":[\n+ {"id":"Otu00001", "metadata":null},\n+ {"id":"Otu00002", "metadata":null},\n+ {"id":"Otu00003", "metadata":null},\n+ {"id":"Otu00004", "metadata":null},\n+ {"id":"Otu00005", "metadata":null},\n+ {"id":"Otu00006", "metadata":null},\n+ {"id":"Otu00007", "metadata":null},\n+ {"id":"Otu00008", "metadata":null},\n+ {"id":"Otu00009", "metadata":null},\n+ {"id":"Otu00010", "metadata":null},\n+ {"id":"Otu00011", "metadata":null},\n+ {"id":"Otu00012", "metadata":null},\n+ {"id":"Otu00013", "metadata":null},\n+ {"id":"Otu00014", "metadata":null},\n+ {"id":"Otu00015", "metadata":null},\n+ {"id":"Otu00016", "metadata":null},\n+ {"id":"Otu00017", "metadata":null},\n+ {"id":"Otu00018", "metadata":null},\n+ {"id":"Otu00019", "metadata":null},\n+ {"id":"Otu00020", "metadata":null},\n+ {"id":"Otu00021", "metadata":null},\n+ {"id":"Otu00022", "metadata":null},\n+ {"id":"Otu00023", "metadata":null},\n+ {"id":"Otu00024", "metadata":null},\n+ {"id":"Otu00025", "metadata":null},\n+ {"id":"Otu00026", "metadata":null},\n+ {"id":"Otu00027", "metadata":null},\n+ {"id":"Otu00028", "metadata":null},\n+ {"id":"Otu00029", "metadata":null},\n+ {"id":"Otu00030", "metadata":null},\n+ {"id":"Otu00031", "metadata":null},\n+ {"id":"Otu00032", "metadata":null},\n+ {"id":"Otu00033", "metadata":null},\n+ {"id":"Otu00034", "metadata":null},\n+ {"id":"Otu00035", "metadata":null},\n+ {"id":"Otu00036", "metadata":null},\n+ {"id":"Otu00037", "metadata":null},\n+ {"id":"Otu00038", "metadata":null},\n+ {"id":"Otu00039", "metadata":null},\n+ {"id":"Otu00040", "metadata":null},\n+ {"id":"Otu00041", "metadata":null},\n+ {"id":"Otu00042", "metadata":null},\n+ {"id":"Otu00043", "metadata":null},\n+ {"id":"Otu00044", "metadata":null},\n+ {"id":"Otu00045", "metadata":null},\n+ {"id":"Otu00046", "metadata":null},\n+ {"id":"Otu00047", "metadata":null},\n+ {"id":"Otu00048", "metadata":null},\n+ {"id":"Otu00049", "metadata":null},\n+ {"id":"Otu00050", "metadata":null},\n+ {"id":"Otu00051", "metadata":null},\n+ {"id":"Otu00052", "metadata":null},\n+ {"id":"Otu00053", "metadata":null},\n+ {"id":"Otu00054", "metadata":null},\n+ {"id":"Otu00055", "metadata":null},\n+ {"id":"Otu00056", "metadata":null},\n+ {"id":"Otu00057", "metadata":null},\n+ {"id":"Otu00058", "metadata":null},\n+ {"id":"Otu00059", "metadata":null},\n+ {"id":"Otu00060", "metadata":null},\n+ {"id":"Otu00061", "metadata":null},\n+ {"id":"Otu00062", "metadata":null},\n+ {"id":"Otu00063", "metadata":null},\n+ {"id":"Otu00064", "metadata":null},\n+ {"id":"Otu00065", "metadata":null},\n+ {"id":"Otu00066", "metadata":null},\n+ {"id":"Otu00067", "metadata":null},\n+ {"id":"Otu00068", "metadata":null},\n+ {"id":"Otu00069", "metadata":null},\n+ {"id":"Otu00070", "metadata":null},\n+ {"id":"Otu00071", "metadata":null},\n+ {"id":"Otu00072", "metadata":null},\n+ {"id":"Otu00073", "metadata":null},\n+ {"id":"Otu00074", "metadata":null},\n+ {"id":"Otu00075", "metadata":null},\n+ {"id":"Otu00076", "metadata":nul'..b' [3827,0,1],\n+ [3828,1,1],\n+ [3829,0,1],\n+ [3830,0,1],\n+ [3831,0,1],\n+ [3832,0,1],\n+ [3833,0,1],\n+ [3834,1,1],\n+ [3835,1,1],\n+ [3836,0,1],\n+ [3837,0,1],\n+ [3838,0,1],\n+ [3839,0,1],\n+ [3840,1,1],\n+ [3841,0,1],\n+ [3842,0,1],\n+ [3843,0,1],\n+ [3844,1,1],\n+ [3845,0,1],\n+ [3846,0,1],\n+ [3847,0,1],\n+ [3848,0,1],\n+ [3849,0,1],\n+ [3850,0,1],\n+ [3851,0,1],\n+ [3852,0,1],\n+ [3853,0,1],\n+ [3854,0,1],\n+ [3855,0,1],\n+ [3856,0,1],\n+ [3857,0,1],\n+ [3858,0,1],\n+ [3859,0,1],\n+ [3860,0,1],\n+ [3861,0,1],\n+ [3862,0,1],\n+ [3863,0,1],\n+ [3864,0,1],\n+ [3865,0,1],\n+ [3866,0,1],\n+ [3867,0,1],\n+ [3868,0,1],\n+ [3869,0,1],\n+ [3870,0,1],\n+ [3871,0,1],\n+ [3872,0,1],\n+ [3873,0,1],\n+ [3874,0,1],\n+ [3875,0,1],\n+ [3876,0,1],\n+ [3877,0,1],\n+ [3878,0,1],\n+ [3879,0,1],\n+ [3880,0,1],\n+ [3881,0,1],\n+ [3882,0,1],\n+ [3883,0,1],\n+ [3884,0,1],\n+ [3885,0,1],\n+ [3886,0,1],\n+ [3887,0,1],\n+ [3888,0,1],\n+ [3889,0,1],\n+ [3890,0,1],\n+ [3891,0,1],\n+ [3892,0,1],\n+ [3893,0,1],\n+ [3894,0,1],\n+ [3895,0,1],\n+ [3896,0,1],\n+ [3897,0,1],\n+ [3898,0,1],\n+ [3899,0,1],\n+ [3900,0,1],\n+ [3901,0,1],\n+ [3902,0,1],\n+ [3903,1,1],\n+ [3904,1,1],\n+ [3905,0,1],\n+ [3906,1,1],\n+ [3907,1,1],\n+ [3908,0,1],\n+ [3909,0,1],\n+ [3910,1,1],\n+ [3911,0,1],\n+ [3912,0,1],\n+ [3913,1,1],\n+ [3914,0,1],\n+ [3915,0,1],\n+ [3916,0,1],\n+ [3917,1,1],\n+ [3918,1,1],\n+ [3919,1,1],\n+ [3920,0,1],\n+ [3921,1,1],\n+ [3922,1,1],\n+ [3923,0,1],\n+ [3924,0,1],\n+ [3925,1,1],\n+ [3926,0,1],\n+ [3927,0,1],\n+ [3928,0,1],\n+ [3929,1,1],\n+ [3930,0,1],\n+ [3931,1,1],\n+ [3932,0,1],\n+ [3933,0,1],\n+ [3934,0,1],\n+ [3935,0,1],\n+ [3936,0,1],\n+ [3937,0,1],\n+ [3938,0,1],\n+ [3939,0,1],\n+ [3940,0,1],\n+ [3941,1,1],\n+ [3942,0,1],\n+ [3943,0,1],\n+ [3944,0,1],\n+ [3945,0,1],\n+ [3946,0,1],\n+ [3947,0,1],\n+ [3948,1,1],\n+ [3949,0,1],\n+ [3950,1,1],\n+ [3951,0,1],\n+ [3952,1,1],\n+ [3953,0,1],\n+ [3954,0,1],\n+ [3955,0,1],\n+ [3956,0,1],\n+ [3957,1,1],\n+ [3958,0,1],\n+ [3959,0,1],\n+ [3960,0,1],\n+ [3961,1,1],\n+ [3962,1,1],\n+ [3963,0,1],\n+ [3964,0,1],\n+ [3965,0,1],\n+ [3966,0,1],\n+ [3967,0,1],\n+ [3968,1,1],\n+ [3969,0,1],\n+ [3970,0,1],\n+ [3971,0,1],\n+ [3972,0,1],\n+ [3973,0,1],\n+ [3974,0,1],\n+ [3975,0,1],\n+ [3976,1,1],\n+ [3977,1,1],\n+ [3978,0,1],\n+ [3979,0,1],\n+ [3980,0,1],\n+ [3981,1,1],\n+ [3982,0,1],\n+ [3983,1,1],\n+ [3984,0,1],\n+ [3985,0,1],\n+ [3986,0,1]]\n+}\n' |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/stool_small.count_table --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.count_table Tue Mar 20 22:19:37 2018 -0400 |
| b |
| @@ -0,0 +1,47 @@ +Representative_Sequence total +F11Fcsw_12747 1 +F11Fcsw_13125 1 +F11Fcsw_13572 2 +F11Fcsw_13584 1 +F11Fcsw_13612 2 +F11Fcsw_13784 2 +F11Fcsw_14513 1 +F11Fcsw_14920 1 +F11Fcsw_14954 1 +F11Fcsw_14980 1 +F11Fcsw_15042 1 +F11Fcsw_15664 1 +F11Fcsw_17394 1 +F11Fcsw_17898 1 +F11Fcsw_18564 1 +F11Fcsw_19115 1 +F11Fcsw_19402 1 +F11Fcsw_19500 1 +F11Fcsw_20028 1 +F11Fcsw_20361 1 +F11Fcsw_20429 1 +F11Fcsw_20462 1 +F11Fcsw_20686 1 +F11Fcsw_21035 1 +F11Fcsw_21196 1 +F11Fcsw_21505 1 +F11Fcsw_21636 1 +F11Fcsw_21645 1 +F11Fcsw_21954 1 +F11Fcsw_22687 1 +F11Fcsw_22831 1 +F11Fcsw_22880 1 +F11Fcsw_22900 1 +F11Fcsw_23043 1 +F11Fcsw_23322 1 +F11Fcsw_23608 1 +F11Fcsw_23684 1 +F11Fcsw_24087 1 +F11Fcsw_24273 1 +F11Fcsw_24701 2 +F11Fcsw_24967 1 +F11Fcsw_25501 1 +F11Fcsw_25574 1 +F11Fcsw_26078 1 +F11Fcsw_26175 1 +F11Fcsw_26418 1 |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/stool_small.denovo.vsearch.accnos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.denovo.vsearch.accnos Tue Mar 20 22:19:37 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +F11Fcsw_21505 +F11Fcsw_23322 |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/stool_small.names --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.names Tue Mar 20 22:19:37 2018 -0400 |
| b |
| @@ -0,0 +1,46 @@ +F11Fcsw_12747 F11Fcsw_12747 +F11Fcsw_13125 F11Fcsw_13125 +F11Fcsw_13572 F11Fcsw_13572,F11Fcsw_14202 +F11Fcsw_13584 F11Fcsw_13584 +F11Fcsw_13612 F11Fcsw_13612,F11Fcsw_23132 +F11Fcsw_13784 F11Fcsw_13784,F11Fcsw_21715 +F11Fcsw_14513 F11Fcsw_14513 +F11Fcsw_14920 F11Fcsw_14920 +F11Fcsw_14954 F11Fcsw_14954 +F11Fcsw_14980 F11Fcsw_14980 +F11Fcsw_15042 F11Fcsw_15042 +F11Fcsw_15664 F11Fcsw_15664 +F11Fcsw_17394 F11Fcsw_17394 +F11Fcsw_17898 F11Fcsw_17898 +F11Fcsw_18564 F11Fcsw_18564 +F11Fcsw_19115 F11Fcsw_19115 +F11Fcsw_19402 F11Fcsw_19402 +F11Fcsw_19500 F11Fcsw_19500 +F11Fcsw_20028 F11Fcsw_20028 +F11Fcsw_20361 F11Fcsw_20361 +F11Fcsw_20429 F11Fcsw_20429 +F11Fcsw_20462 F11Fcsw_20462 +F11Fcsw_20686 F11Fcsw_20686 +F11Fcsw_21035 F11Fcsw_21035 +F11Fcsw_21196 F11Fcsw_21196 +F11Fcsw_21505 F11Fcsw_21505 +F11Fcsw_21636 F11Fcsw_21636 +F11Fcsw_21645 F11Fcsw_21645 +F11Fcsw_21954 F11Fcsw_21954 +F11Fcsw_22687 F11Fcsw_22687 +F11Fcsw_22831 F11Fcsw_22831 +F11Fcsw_22880 F11Fcsw_22880 +F11Fcsw_22900 F11Fcsw_22900 +F11Fcsw_23043 F11Fcsw_23043 +F11Fcsw_23322 F11Fcsw_23322 +F11Fcsw_23608 F11Fcsw_23608 +F11Fcsw_23684 F11Fcsw_23684 +F11Fcsw_24087 F11Fcsw_24087 +F11Fcsw_24273 F11Fcsw_24273 +F11Fcsw_24701 F11Fcsw_24701,F11Fcsw_24794 +F11Fcsw_24967 F11Fcsw_24967 +F11Fcsw_25501 F11Fcsw_25501 +F11Fcsw_25574 F11Fcsw_25574 +F11Fcsw_26078 F11Fcsw_26078 +F11Fcsw_26175 F11Fcsw_26175 +F11Fcsw_26418 F11Fcsw_26418 |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/stool_small.unique.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.unique.fasta Tue Mar 20 22:19:37 2018 -0400 |
| b |
| b'@@ -0,0 +1,92 @@\n+>F11Fcsw_12747\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGCAGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATCAGATATGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATCCCAGAGATGCCTCCAAAATACATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGG\n+>F11Fcsw_13125\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGACCCATCGTAAAGCGATAGCTTACAAGTAGAGGCCATCTTTAGTCGAGCTTCCATGCGGAAGTTCGACAACATTCGGTATTAGCAGTCCTTTCGAACTGTTGTCCCCATCTTTACGG\n+>F11Fcsw_13572\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAAA\n+>F11Fcsw_13584\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGATGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGGTTATCGAAATTCTTTAATAACAAGAAGATGCCTTCTCGTTATACTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCGGAATAACCGGTAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAACCTA\n+>F11Fcsw_13612\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGTCCGTGTCTCAGTACCAATGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCCCAACTAGCTAATGCGCCGCATGCCCATCCCTGTCCGGATTACTCCTTTGGCGCTCGCAGGATGCCCCGCAAACGCTTTATGCGATATTAGACCGGATTTCTCCGGATTATCCCTCTGACAGGGGCAGGTTGCATACGTGTTACTCACCCG\n+>F11Fcsw_13784\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG\n+>F11Fcsw_14513\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGATCACCCTCTCAGGTCGGCTAACCATCGTCGACTTGGTAGTCCGTTACACTACCAACTATCTAATGGTACGCGAGCCCATCCACATCCGATAAATCTTTTACCCCTGAGAGATGCCTCTCTGTGGTCTTATGCGGTATTAGCACACATTTCTATGTGTTATTCCCCAGATGTGGGCAGGTTG\n+>F11Fcsw_14920\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTGAGCCATTACCTCTCCAACTAGCTAATCAGACGCGGGCCCATCCTATACCACCTGAGTTTTTCCTACCGTATCATGCGGTACTGTAGGCTTATGCGGTTTTAGCACAGATTTCTCTGTGTTATCCCCTGTATAGGGCAGGTTACCCACGCGTTT\n+>F11Fcsw_14954\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCGGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATGTCCGGGATGCCCCGGTCATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACGCGTTACT\n+>F11Fcsw_14980\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTTTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGATCGGCTACCCATCGTCGCCTTGGTGAGCCGTTACCTCTCCAACTAGCTAATGGGCCGCGAGCCCCTCCTATACCGCCTCAGCTTTTACCCCTCTCCGATGCCGGAGTGTGGTCTTATACCGTATTAGCACAAATTTCTCTGTGTTATCCCGTTGTATAGGATAGGTTGCTCACGTGTTACTCACCCG\n+>F11Fcsw_15042\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCGCCCTCTCAGGCCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGCCCATCCCATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCGTTTCCAGCTGTTATCCCCCGGTATGGGGCAGGTCACCCACGCGTTACT\n+>F11Fcsw_15664\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTACT\n+>F11Fcsw_17394\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTTGCCTTGGTAGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTCACACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTATGCGGTATTATCAGCCGTTTCCAACTGCTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTA\n+>F11Fcsw_17898\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGTATCATGCGATACCGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCGTTACTCACCCG\n+>F11Fcsw_18564\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCA'..b'GCAGCTCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCG\n+>F11Fcsw_22900\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATTCACGCGTTACTCACCCG\n+>F11Fcsw_23043\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTA\n+>F11Fcsw_23322\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCCGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCGCCAA\n+>F11Fcsw_23608\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTAGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCG\n+>F11Fcsw_23684\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCCCTTTCAGATGTCTTCTAGAGACGTCATTGGGTATTAGTCTTACTTTCGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCGTGCG\n+>F11Fcsw_24087\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACAAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACG\n+>F11Fcsw_24273\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTAGGCCGTTACCCCACCAACTATCTAATCAGACGCGAGCCCATCTATCAGCGGATTACTCCTTTCCCACTTTCATCATGTGATATTTATTGGCATATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCCTGATAGGCG\n+>F11Fcsw_24701\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCG\n+>F11Fcsw_24967\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT\n+>F11Fcsw_25501\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCAGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATTTCGACCATGCGATCAAAATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACG\n+>F11Fcsw_25574\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGAAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG\n+>F11Fcsw_26078\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTATCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCA\n+>F11Fcsw_26175\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG\n+>F11Fcsw_26418\n+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTGTACAGGGCAGGTTACCCACGCGTTACT\n' |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb test-data/stool_small.vsearch.chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stool_small.vsearch.chimeras Tue Mar 20 22:19:37 2018 -0400 |
| b |
| @@ -0,0 +1,47 @@ +Score Query ParentA ParentB IdQM IdQA IdQB IdAB IdQT LY LN LA RY RN RA Div YN +0.0000 F11Fcsw_13572;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_13612;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_13784;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_24701;size=2; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_12747;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0514 F11Fcsw_13125;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13784;size=2; 80.5 77.1 80.1 72.7 80.1 21 20 19 8 0 6 0.4 N +0.1560 F11Fcsw_13584;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; 82.5 80.4 72.9 73.3 80.4 23 0 8 15 10 24 2.1 N +0.0259 F11Fcsw_14513;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 82.7 79.3 81.4 81.9 81.4 11 8 11 11 3 19 1.3 N +0.0550 F11Fcsw_14920;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 84.7 83.5 76.3 80.9 83.5 23 3 21 5 2 10 1.3 N +0.0000 F11Fcsw_14954;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0216 F11Fcsw_14980;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 82.0 79.1 80.8 82.4 80.8 7 4 6 12 5 28 1.3 N +0.0400 F11Fcsw_15042;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 84.6 82.9 79.1 79.9 82.9 21 8 18 5 1 9 1.7 N +0.0524 F11Fcsw_15664;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 84.6 83.8 71.7 72.9 83.8 41 10 25 3 1 1 0.8 N +0.0000 F11Fcsw_17394;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0428 F11Fcsw_17898;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 86.7 86.2 71.7 72.5 86.2 45 9 21 2 1 1 0.4 N +0.0000 F11Fcsw_18564;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19115;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19402;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_19500;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0158 F11Fcsw_20028;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 77.8 77.4 70.4 73.0 77.4 32 15 35 1 0 1 0.4 N +0.0161 F11Fcsw_20361;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13784;size=2; 77.5 71.4 77.1 73.1 77.1 2 1 3 28 14 33 0.4 N +0.1919 F11Fcsw_20429;size=1; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; 84.6 82.1 75.4 73.3 82.1 22 0 5 16 10 22 2.5 N +0.0158 F11Fcsw_20462;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 77.8 77.4 70.4 73.0 77.4 32 15 35 1 0 1 0.4 N +0.0000 F11Fcsw_20686;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0422 F11Fcsw_21035;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_13784;size=2; 86.3 84.6 81.3 82.2 84.6 16 4 4 8 4 21 1.7 N +0.0000 F11Fcsw_21196;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.5878 F11Fcsw_21505;size=1; F11Fcsw_13572;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 92.4 76.7 88.2 72.1 88.2 11 0 0 48 7 13 4.2 Y +0.0000 F11Fcsw_21636;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_21645;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_21954;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_22687;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_22831;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0322 F11Fcsw_22880;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.3 82.9 70.8 72.5 82.9 41 11 27 2 1 1 0.4 N +0.0000 F11Fcsw_22900;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_23043;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.5123 F11Fcsw_23322;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 99.2 83.0 97.9 81.7 97.9 3 0 1 40 1 0 1.2 Y +0.0000 F11Fcsw_23608;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_23684;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0324 F11Fcsw_24087;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.8 83.3 71.2 72.5 83.3 41 11 26 2 1 1 0.4 N +0.0000 F11Fcsw_24273;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_24967;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0000 F11Fcsw_25501;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0461 F11Fcsw_25574;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 84.9 80.8 82.0 82.4 82.0 12 5 3 14 4 24 2.9 N +0.0000 F11Fcsw_26078;size=1; * * * * * * * * 0 0 0 0 0 0 * N +0.0509 F11Fcsw_26175;size=1; F11Fcsw_13784;size=2; F11Fcsw_24701;size=2; F11Fcsw_24701;size=2; 85.8 81.2 82.8 82.4 82.8 12 5 3 15 4 22 2.9 N +0.0696 F11Fcsw_26418;size=1; F11Fcsw_13784;size=2; F11Fcsw_13572;size=2; F11Fcsw_13784;size=2; 83.3 82.1 72.5 72.9 82.1 38 12 27 3 0 1 1.2 N |
| b |
| diff -r 06c8f1be0f31 -r 506ad7182cfb tree.shared.xml --- a/tree.shared.xml Tue Sep 05 16:53:53 2017 -0400 +++ b/tree.shared.xml Tue Mar 20 22:19:37 2018 -0400 |
| [ |
| @@ -7,52 +7,52 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$input.dist" input_dist.dat && - #if not $input.source == "shared": - ln -s "$input.name" input_name.dat && - #end if +## create symlinks to input datasets +ln -s '$input.dist' input_dist.dat && +#if not $input.source == "shared": + ln -s '$input.name' input_name.dat && +#end if - echo 'tree.shared( - #if $input.source == "shared": - shared=input_dist.dat, - #if $input.groups: - groups=${ str($input.groups).replace(",","-") }, - #end if - #if $input.label: - label=${ str($input.label).replace(",","-") }, - #end if - #if $input.subsampling.use == "yes": - #if $input.subsampling.subsample: - subsample=$input.subsampling.subsample, - #else - subsample=T, - #end if - #if $input.subsampling.iters: - iters="$input.subsampling.iters, - #end if - #end if - #elif $input.source == "column": - column=input_dist.dat, - name=input_name.dat, - #elif $input.source == "phylip": - phylip=input_dist.dat, - #if $input.name: - name=input_name.dat, - #end if +echo 'tree.shared( + #if $input.source == "shared": + shared=input_dist.dat, + #if $input.groups: + groups=${ str($input.groups).replace(",","-") }, + #end if + #if $input.label: + label=${ str($input.label).replace(",","-") }, + #end if + #if $input.subsampling.use == "yes": + #if $input.subsampling.subsample: + subsample=$input.subsampling.subsample, #else - count=input_name.dat, + subsample=T, #end if - #if $calc: - calc=${ str($calc).replace(",","-") }, + #if $input.subsampling.iters: + iters="$input.subsampling.iters, #end if - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log + #end if + #elif $input.source == "column": + column=input_dist.dat, + name=input_name.dat, + #elif $input.source == "phylip": + phylip=input_dist.dat, + #if $input.name: + name=input_name.dat, + #end if + #else + count=input_name.dat, + #end if + #if $calc: + calc=${ str($calc).replace(",","-") }, + #end if + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -105,6 +105,7 @@ <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option> <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option> </param> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -121,6 +122,7 @@ <param name="source" value="phylip"/> <param name="dist" value="env.dist"/> <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with shared and subsampling --> @@ -131,6 +133,7 @@ <output_collection name="trefiles" count="108"> <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with shared and label and group select and all calculators --> @@ -142,6 +145,7 @@ <output_collection name="trefiles" count="117"> <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/> </output_collection> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with column and name file --> @@ -149,11 +153,11 @@ <param name="dist" value="amazon.pair.dist"/> <param name="name" value="amazon1.names"/> <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -163,7 +167,6 @@ .. _tree.shared: https://www.mothur.org/wiki/Tree.shared -]]> - </help> + ]]></help> <expand macro="citations"/> </tool> |