| Previous changeset 8:738474880da8 (2024-11-16) Next changeset 10:9b3e1acc3ad0 (2025-11-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit f32c3d9a92dca8a60504824fc7bcee290c30a211 |
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added:
test-data/output_metadata.tsv test-data/output_otu_long.tsv test-data/output_otu_short.tsv test-data/output_otu_taxonomy_mapping.tsv test-data/output_phyloseq.rds |
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| diff -r 738474880da8 -r 5029fd9d572e test-data/output_metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_metadata.tsv Tue Apr 01 10:03:02 2025 +0000 |
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| @@ -0,0 +1,68 @@ + SampleID Plant Date Year Period +16SAMP-747 16SAMP-747 Aalborg East 2010-02-04 2010 Winter +16S-AMP-1168 16S-AMP-1168 Aalborg West 2013-05-06 2013 Spring +16SAMP-4603 16SAMP-4603 Aalborg East 2014-08-19 2014 Summer +16S-AMP-1149 16S-AMP-1149 Aalborg East 2013-10-28 2013 Fall +16SAMP-537 16SAMP-537 Aalborg West 2010-08-19 2010 Summer +16S-AMP-1114 16S-AMP-1114 Aalborg West 2013-02-04 2013 Winter +16SAMP-3893 16SAMP-3893 Aalborg East 2014-02-06 2014 Winter +16SAMP-703 16SAMP-703 Aalborg East 2006-02-04 2006 Winter +16SAMP-638 16SAMP-638 Aalborg East 2012-10-28 2012 Fall +16SAMP-2611 16SAMP-2611 Aalborg East 2011-02-04 2011 Winter +16S-AMP-1100 16S-AMP-1100 Aalborg West 2012-08-19 2012 Summer +16SAMP-608 16SAMP-608 Aalborg East 2011-10-28 2011 Fall +16SAMP-636 16SAMP-636 Aalborg East 2012-05-06 2012 Spring +16SAMP-13288 16SAMP-13288 Aalborg West 2015-02-09 2015 Winter +16SAMP-719 16SAMP-719 Aalborg East 2007-08-19 2007 Summer +16S-AMP-1098 16S-AMP-1098 Aalborg West 2012-02-04 2012 Winter +16SAMP-536 16SAMP-536 Aalborg West 2010-05-06 2010 Spring +16S-AMP-1169 16S-AMP-1169 Aalborg West 2013-08-19 2013 Summer +16SAMP-635 16SAMP-635 Aalborg East 2012-02-04 2012 Winter +16SAMP-637 16SAMP-637 Aalborg East 2012-08-19 2012 Summer +16SAMP-717 16SAMP-717 Aalborg East 2007-02-04 2007 Winter +16S-AMP-1148 16S-AMP-1148 Aalborg East 2013-08-19 2013 Summer +16SAMP-735 16SAMP-735 Aalborg West 2008-05-06 2008 Spring +16SAMP-729 16SAMP-729 Aalborg East 2008-08-19 2008 Summer +16SAMP-738 16SAMP-738 Aalborg East 2009-02-04 2009 Winter +16SAMP-2613 16SAMP-2613 Aalborg West 2011-08-19 2011 Summer +16SAMP-10925 16SAMP-10925 Aalborg East 2015-10-27 2015 Fall +16SAMP-3913 16SAMP-3913 Aalborg East 2014-07-03 2014 Summer +16SAMP-716 16SAMP-716 Aalborg West 2006-02-04 2006 Winter +16SAMP-726 16SAMP-726 Aalborg West 2007-08-19 2007 Summer +16SAMP-728 16SAMP-728 Aalborg East 2008-05-06 2008 Spring +16SAMP-625 16SAMP-625 Aalborg West 2011-02-04 2011 Winter +16SAMP-736 16SAMP-736 Aalborg West 2008-08-19 2008 Summer +16SAMP-13281 16SAMP-13281 Aalborg East 2015-02-10 2015 Winter +16SAMP-626 16SAMP-626 Aalborg West 2011-10-28 2011 Fall +16SAMP-704 16SAMP-704 Aalborg East 2006-05-06 2006 Spring +16SAMP-2612 16SAMP-2612 Aalborg East 2011-08-19 2011 Summer +16SAMP-746 16SAMP-746 Aalborg West 2009-05-06 2009 Spring +16SAMP-522 16SAMP-522 Aalborg East 2010-10-28 2010 Fall +16SAMP-516 16SAMP-516 Aalborg West 2009-10-28 2009 Fall +16S-AMP-1170 16S-AMP-1170 Aalborg West 2013-10-28 2013 Fall +16S-AMP-1099 16S-AMP-1099 Aalborg West 2012-05-06 2012 Spring +16SAMP-10932 16SAMP-10932 Aalborg West 2015-10-27 2015 Fall +16SAMP-740 16SAMP-740 Aalborg East 2009-10-28 2009 Fall +16SAMP-739 16SAMP-739 Aalborg East 2009-05-06 2009 Spring +16SAMP-4597 16SAMP-4597 Aalborg West 2014-05-05 2014 Spring +16SAMP-535 16SAMP-535 Aalborg West 2010-02-04 2010 Winter +16SAMP-3941 16SAMP-3941 Aalborg West 2014-08-18 2014 Summer +16SAMP-3953 16SAMP-3953 Aalborg West 2014-11-12 2014 Fall +16SAMP-720 16SAMP-720 Aalborg East 2007-10-28 2007 Fall +16SAMP-705 16SAMP-705 Aalborg East 2006-08-19 2006 Summer +16SAMP-10907 16SAMP-10907 Aalborg East 2015-08-24 2015 Summer +16SAMP-538 16SAMP-538 Aalborg West 2010-10-28 2010 Fall +16SAMP-10911 16SAMP-10911 Aalborg West 2015-08-24 2015 Summer +16SAMP-737 16SAMP-737 Aalborg West 2008-10-28 2008 Fall +16SAMP-4591 16SAMP-4591 Aalborg West 2014-02-04 2014 Winter +16SAMP-745 16SAMP-745 Aalborg West 2009-02-04 2009 Winter +16SAMP-706 16SAMP-706 Aalborg East 2006-10-28 2006 Fall +16SAMP-3946 16SAMP-3946 Aalborg East 2014-11-13 2014 Fall +16S-AMP-1101 16S-AMP-1101 Aalborg West 2012-10-28 2012 Fall +16SAMP-10896 16SAMP-10896 Aalborg West 2015-05-04 2015 Spring +16SAMP-10891 16SAMP-10891 Aalborg East 2015-05-04 2015 Spring +16SAMP-748 16SAMP-748 Aalborg East 2010-05-06 2010 Spring +16SAMP-725 16SAMP-725 Aalborg West 2007-02-04 2007 Winter +16SAMP-730 16SAMP-730 Aalborg East 2008-10-28 2008 Fall +16S-AMP-1107 16S-AMP-1107 Aalborg East 2013-05-06 2013 Spring +16SAMP-727 16SAMP-727 Aalborg East 2008-02-04 2008 Winter |
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| diff -r 738474880da8 -r 5029fd9d572e test-data/output_otu_long.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_otu_long.tsv Tue Apr 01 10:03:02 2025 +0000 |
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| b'@@ -0,0 +1,201 @@\n+OTU\t16SAMP-747\t16S-AMP-1168\t16SAMP-4603\t16S-AMP-1149\t16SAMP-537\t16S-AMP-1114\t16SAMP-3893\t16SAMP-703\t16SAMP-638\t16SAMP-2611\t16S-AMP-1100\t16SAMP-608\t16SAMP-636\t16SAMP-13288\t16SAMP-719\t16S-AMP-1098\t16SAMP-536\t16S-AMP-1169\t16SAMP-635\t16SAMP-637\t16SAMP-717\t16S-AMP-1148\t16SAMP-735\t16SAMP-729\t16SAMP-738\t16SAMP-2613\t16SAMP-10925\t16SAMP-3913\t16SAMP-716\t16SAMP-726\t16SAMP-728\t16SAMP-625\t16SAMP-736\t16SAMP-13281\t16SAMP-626\t16SAMP-704\t16SAMP-2612\t16SAMP-746\t16SAMP-522\t16SAMP-516\t16S-AMP-1170\t16S-AMP-1099\t16SAMP-10932\t16SAMP-740\t16SAMP-739\t16SAMP-4597\t16SAMP-535\t16SAMP-3941\t16SAMP-3953\t16SAMP-720\t16SAMP-705\t16SAMP-10907\t16SAMP-538\t16SAMP-10911\t16SAMP-737\t16SAMP-4591\t16SAMP-745\t16SAMP-706\t16SAMP-3946\t16S-AMP-1101\t16SAMP-10896\t16SAMP-10891\t16SAMP-748\t16SAMP-725\t16SAMP-730\t16S-AMP-1107\t16SAMP-727\tKingdom\tPhylum\tClass\tOrder\tFamily\tGenus\tSpecies\n+OTU_95\t1\t132\t382\t37\t2\t29\t317\t2\t241\t5\t15\t379\t422\t111\t1\t47\t0\t101\t603\t151\t2\t350\t0\t0\t0\t7\t527\t576\t0\t2\t0\t5\t0\t324\t182\t5\t31\t0\t1\t0\t54\t22\t108\t0\t1\t102\t0\t203\t289\t3\t33\t274\t0\t291\t0\t94\t0\t2\t711\t165\t23\t578\t27\t0\t0\t88\t0\tk__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Bdellovibrionales\tf__Bdellovibrionaceae\tg__OM27 clade\ts__\n+OTU_173\t124\t32\t13\t24\t14\t45\t15\t86\t50\t608\t31\t80\t280\t72\t47\t44\t1\t17\t144\t52\t48\t86\t2\t46\t65\t36\t3\t62\t2\t1\t128\t40\t2\t2\t22\t88\t61\t9\t56\t2\t25\t35\t19\t100\t258\t36\t0\t14\t20\t12\t32\t1\t6\t36\t2\t35\t13\t40\t1\t27\t27\t17\t275\t2\t30\t142\t17\tk__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__uncultured\ts__\n+OTU_318\t77\t38\t15\t95\t14\t52\t157\t43\t37\t131\t2\t33\t138\t49\t30\t24\t15\t5\t97\t26\t78\t43\t16\t11\t110\t11\t17\t179\t57\t1\t20\t28\t0\t176\t2\t123\t34\t45\t43\t3\t19\t26\t9\t40\t107\t16\t23\t4\t6\t22\t20\t8\t6\t11\t7\t32\t24\t24\t17\t26\t24\t227\t215\t61\t42\t237\t66\tk__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Burkholderiales\tf__Comamonadaceae\tg__Simplicispira\ts__\n+OTU_4382\t16\t90\t95\t57\t39\t49\t23\t12\t32\t51\t57\t61\t83\t158\t20\t65\t10\t93\t69\t32\t34\t48\t8\t15\t21\t68\t68\t39\t33\t15\t37\t18\t6\t12\t87\t19\t51\t27\t24\t22\t75\t44\t113\t55\t11\t107\t20\t84\t55\t18\t34\t36\t21\t159\t18\t64\t16\t27\t35\t90\t67\t28\t41\t23\t21\t32\t9\tk__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Rhodocyclales\tf__Rhodocyclaceae\tg__Sulfuritalea\ts__\n+OTU_233\t39\t23\t23\t65\t12\t37\t27\t35\t57\t27\t29\t82\t49\t19\t46\t48\t12\t18\t34\t115\t29\t29\t32\t60\t20\t39\t86\t5\t8\t23\t32\t24\t31\t9\t32\t17\t82\t34\t15\t39\t33\t21\t21\t48\t10\t11\t9\t14\t5\t48\t17\t41\t22\t19\t62\t12\t29\t51\t28\t43\t19\t34\t26\t14\t34\t40\t54\tk__Bacteria\tp__Actinobacteria\tc__Thermoleophilia\to__Solirubrobacterales\tf__480-2\tg__K2-78\ts__\n+OTU_81\t37\t31\t74\t117\t16\t24\t32\t6\t18\t27\t8\t68\t76\t98\t19\t25\t11\t9\t65\t28\t38\t49\t7\t13\t14\t20\t71\t24\t25\t12\t26\t8\t4\t192\t38\t12\t20\t19\t12\t11\t4\t30\t13\t34\t17\t17\t13\t9\t17\t20\t54\t45\t11\t34\t25\t13\t14\t76\t56\t15\t23\t116\t27\t39\t12\t47\t7\tk__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Saprospiraceae\tg__CYCU-0281\ts__\n+OTU_161\t21\t12\t12\t16\t30\t21\t21\t28\t9\t32\t20\t16\t16\t5\t29\t16\t33\t13\t9\t12\t22\t7\t58\t39\t26\t35\t13\t19\t50\t82\t49\t25\t45\t7\t15\t22\t22\t42\t15\t33\t13\t22\t8\t32\t24\t15\t32\t12\t11\t32\t34\t5\t26\t11\t45\t15\t39\t34\t22\t24\t7\t18\t58\t46\t11\t20\t25\tk__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhizobiales\tf__Hyphomicrobiaceae\tg__Hyphomicrobium\ts__\n+OTU_289\t0\t104\t58\t25\t2\t10\t28\t0\t39\t3\t18\t32\t37\t106\t6\t40\t2\t28\t58\t37\t8\t52\t2\t1\t0\t13\t86\t39\t2\t0\t4\t6\t0\t101\t47\t10\t20\t5\t5\t1\t37\t15\t55\t2\t0\t12\t0\t41\t45\t4\t3\t59\t0\t76\t0\t74\t1\t24\t19\t35\t44\t39\t6\t3\t0\t8\t0\tk__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Chitinophagaceae\tg__uncultured\ts__\n+OTU_6255\t48\t3\t14\t29\t6\t13\t9\t15\t25\t22\t3\t27\t27\t9\t14\t8\t3\t8\t20\t21\t6\t22\t9\t36\t40\t13\t16\t9\t2\t8\t20\t3\t8\t7\t4\t8\t31\t13\t33\t7\t12\t7\t4\t50\t17\t5\t5\t2\t1\t32\t20\t10\t7\t3\t6\t9\t11\t18\t11\t6\t5\t28\t48\t6\t36\t18\t40\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Clostridiaceae 1\tg__Proteiniclasticum\ts__\n+OTU_541\t0\t14\t18\t4\t4\t18\t15\t3\t17\t12\t18\t22\t16\t66\t23\t9\t7\t24\t14\t24\t7\t3\t6\t3\t2\t17\t67\t17\t6\t10\t5\t12\t1\t22\t19\t5\t11\t8\t5\t13\t9\t15\t36\t9\t5\t17\t7\t11\t12\t2\t6\t42\t4\t27\t5\t13\t4\t14\t11\t19\t45\t45\t3\t17\t1\t7\t0\tk__Bacteria\tp__Acidobacteria\tc__Acidobacteria\to__Subgroup 6\tf__\tg__\ts__\n+OTU_448\t1\t3\t103\t13\t0\t3\t15\t1\t0\t14\t4\t1\t0\t34\t34\t2\t0\t4\t1\t0\t39\t3\t0\t7\t2\t26\t81\t20\t0\t5\t2\t0\t0\t11\t2\t0\t68\t1\t0\t0\t8\t2\t10\t28\t3\t2\t0\t6\t13\t16\t7\t96\t0\t13\t2\t8\t1\t3'..b'idetes\tc__Bacteroidia\to__Bacteroidales\tf__Porphyromonadaceae\tg__Parabacteroides\ts__\n+OTU_9228\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Clostridiaceae 1\tg__Clostridium sensu stricto 6\ts__\n+OTU_14146\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Bacteroidetes\tc__Bacteroidia\to__Bacteroidales\tf__Prevotellaceae\tg__Prevotellaceae UCG-004\ts__\n+OTU_6507\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Elusimicrobia\tc__Elusimicrobia\to__Lineage IIb\tf__\tg__\ts__\n+OTU_8708\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\t\t\t\t\t\t\n+OTU_9665\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Actinobacteria\tc__Acidimicrobiia\to__Acidimicrobiales\t\t\t\n+OTU_6422\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Chitinophagaceae\tg__Parafilimonas\ts__\n+OTU_5187\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\tk__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__uncultured\ts__\n+OTU_1543\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Saccharibacteria\tc__\to__\tf__\tg__\ts__\n+OTU_11781\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Actinobacteria\tc__Coriobacteriia\to__Coriobacteriales\tf__Coriobacteriaceae\tg__Atopobium\ts__\n+OTU_10321\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Rhodospirillaceae\tg__Defluviicoccus\ts__cluster I\n+OTU_6237\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\tk__Bacteria\tp__Verrucomicrobia\tc__OPB35 soil group\to__\tf__\tg__\ts__\n+OTU_8887\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\tk__Bacteria\tp__Tenericutes\tc__Mollicutes\to__Mollicutes 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| diff -r 738474880da8 -r 5029fd9d572e test-data/output_otu_short.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_otu_short.tsv Tue Apr 01 10:03:02 2025 +0000 |
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\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\n+OTU_12690\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+OTU_3161\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+OTU_11903\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\n+OTU_3824\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\n+OTU_11294\t0\t0\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n' |
| b |
| diff -r 738474880da8 -r 5029fd9d572e test-data/output_otu_taxonomy_mapping.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_otu_taxonomy_mapping.tsv Tue Apr 01 10:03:02 2025 +0000 |
| [ |
| b'@@ -0,0 +1,201 @@\n+OTU\tPhylum\tClass\tOrder\tFamily\tGenus\tSpecies\n+OTU_8735\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnospiraceae\tg__Acetitomaculum\ts__\n+OTU_13382\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminococcaceae UCG-005\ts__\n+OTU_5516\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\tf__Cytophagaceae\tg__Dyadobacter\ts__\n+OTU_8315\tp__Proteobacteria\tc__Betaproteobacteria\to__Nitrosomonadales\tf__Nitrosomonadaceae\tg__Nitrosomonas\ts__\n+OTU_10522\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Intrasporangiaceae\tg__Tetrasphaera\ts__\n+OTU_11040\tp__Proteobacteria\tc__Gammaproteobacteria\to__Xanthomonadales\tf__Xanthomonadaceae\t\t\n+OTU_7263\tp__Proteobacteria\tc__Deltaproteobacteria\to__Desulfobacterales\tf__Desulfobacteraceae\tg__Desulforegula\ts__\n+OTU_13379\tp__Firmicutes\tc__Bacilli\to__Bacillales\tf__Planococcaceae\tg__Rummeliibacillus\ts__\n+OTU_1418\tp__Hydrogenedentes\tc__\to__\tf__\tg__\ts__\n+OTU_556\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnospiraceae\tg__Fusicatenibacter\ts__\n+OTU_6869\tp__Parcubacteria\tc__\to__\tf__\tg__\ts__\n+OTU_10171\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminiclostridium 1\ts__\n+OTU_2830\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Dermatophilaceae\tg__uncultured\ts__\n+OTU_4232\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__AKYH767\tg__\ts__\n+OTU_12831\tp__Planctomycetes\tc__Planctomycetacia\to__Planctomycetales\tf__Planctomycetaceae\t\t\n+OTU_613\tp__Acidobacteria\tc__Holophagae\to__Holophagales\tf__Holophagaceae\t\t\n+OTU_3625\tp__Actinobacteria\tc__Actinobacteria\to__Propionibacteriales\tf__Propionibacteriaceae\tg__Brooklawnia\ts__\n+OTU_3605\tp__Chloroflexi\tc__Chloroflexia\to__Chloroflexales\tf__Roseiflexaceae\tg__\ts__\n+OTU_11148\tp__Actinobacteria\tc__Actinobacteria\to__PeM15\tf__PeM15\tg__\ts__\n+OTU_656\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__uncultured\ts__\n+OTU_4382\tp__Proteobacteria\tc__Betaproteobacteria\to__Rhodocyclales\tf__Rhodocyclaceae\tg__Sulfuritalea\ts__\n+OTU_3834\t\t\t\t\t\t\n+OTU_13127\tp__Firmicutes\tc__Clostridia\to__Clostridiales\t\t\t\n+OTU_4528\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\t\t\t\n+OTU_4485\tp__Proteobacteria\tc__Deltaproteobacteria\to__Myxococcales\tf__Blfdi19\tg__\ts__\n+OTU_12265\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Lactobacillaceae\tg__Lactobacillus\ts__\n+OTU_11820\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\n+OTU_4093\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\n+OTU_8360\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Flavobacteriaceae\tg__Flavobacterium\ts__\n+OTU_15123\tp__Firmicutes\tc__Negativicutes\to__Selenomonadales\tf__Veillonellaceae\t\t\n+OTU_11928\tp__Proteobacteria\tc__Deltaproteobacteria\to__Desulfobacterales\tf__Desulfobacteraceae\t\t\n+OTU_11334\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Acetobacteraceae\tg__Acidicaldus\ts__\n+OTU_4511\tp__Proteobacteria\tc__Deltaproteobacteria\to__Myxococcales\tf__mle1-27\tg__\ts__\n+OTU_3265\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\n+OTU_2991\tp__Actinobacteria\t\t\t\t\t\n+OTU_522\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__Candidatus Defluviifilum\ts__\n+OTU_11832\tp__Proteobacteria\tc__Betaproteobacteria\to__Nitrosomonadales\tf__Nitrosomonadaceae\tg__Nitrosomonas\ts__\n+OTU_6358\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminococcaceae UCG-010\ts__\n+OTU_3611\tp__Saccharibacteria\tc__Unknown Class\to__Unknown Order\tf__SBR2060\tg__SBR2113\ts__\n+OTU_1408\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\t\t\t\n+OTU_7471\tp__Bacteroidetes\t\t\t\t\t\n+OTU_14124\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Subdoligranulum\ts__\n+OTU_13012\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Lactobacillaceae\tg__Lactobacillus\ts__\n+OTU_8113\tp__Candidate division SR1\tc__\to__\tf__\tg__\ts__\n+OTU_11414\tp__Cyanobacteria\tc__Cyanobacteria\to__SubsectionIII\tf__FamilyI\t\t\n+OTU_2232\tp__Actinobacteria\tc__Actinobacteria\to__'..b'_Betaproteobacteria\to__Rhodocyclales\tf__Rhodocyclaceae\tg__Uliginosibacterium\ts__\n+OTU_2244\tp__Chloroflexi\tc__WCHB1-50\to__WCHB1-50\tf__WCHB1-50\tg__WCHB1-50\ts__\n+OTU_7867\tp__Bacteroidetes\tc__BSV13\to__\tf__\tg__\ts__\n+OTU_14248\tp__Actinobacteria\tc__Thermoleophilia\to__Solirubrobacterales\tf__480-2\tg__K2-78\ts__\n+OTU_12704\tp__Proteobacteria\tc__Deltaproteobacteria\to__Myxococcales\tf__bacteriap25\tg__\ts__\n+OTU_364\tp__Chloroflexi\tc__Thermomicrobia\to__JG30-KF-CM45\tf__\tg__\ts__\n+OTU_8245\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Christensenellaceae\tg__Christensenellaceae R-7 group\ts__\n+OTU_10847\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\n+OTU_1151\tp__Acidobacteria\tc__Holophagae\to__Holophagales\tf__Holophagaceae\t\t\n+OTU_1998\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Intrasporangiaceae\tg__Fodinibacter\ts__\n+OTU_10321\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Rhodospirillaceae\tg__Defluviicoccus\ts__cluster I\n+OTU_4721\tp__Proteobacteria\tc__Betaproteobacteria\to__Burkholderiales\tf__Comamonadaceae\tg__Acidovorax\ts__\n+OTU_6237\tp__Verrucomicrobia\tc__OPB35 soil group\to__\tf__\tg__\ts__\n+OTU_1972\tp__Saccharibacteria\tc__Unknown Class\to__FW73\t\t\t\n+OTU_11364\tp__Elusimicrobia\tc__Elusimicrobia\to__Lineage IIb\tf__\tg__\ts__\n+OTU_1816\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Beutenbergiaceae\tg__Salana\ts__\n+OTU_14842\tp__Actinobacteria\tc__Actinobacteria\to__Propionibacteriales\tf__Propionibacteriaceae\tg__Propionimicrobium\ts__\n+OTU_6533\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Leptotrichiaceae\tg__uncultured\ts__\n+OTU_8887\tp__Tenericutes\tc__Mollicutes\to__Mollicutes RF9\tf__\tg__\ts__\n+OTU_12690\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__Litorilinea\ts__\n+OTU_3097\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Clostridiaceae 1\tg__Proteiniclasticum\ts__\n+OTU_3257\tp__Firmicutes\tc__Erysipelotrichia\to__Erysipelotrichales\tf__Erysipelotrichaceae\tg__Faecalitalea\ts__\n+OTU_3161\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Acetobacteraceae\tg__uncultured\ts__\n+OTU_11903\tp__Actinobacteria\tc__Thermoleophilia\to__Solirubrobacterales\tf__480-2\tg__\ts__\n+OTU_7508\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminiclostridium 5\ts__\n+OTU_10969\tp__Proteobacteria\tc__Deltaproteobacteria\to__Oligoflexales\tf__\tg__\ts__\n+OTU_1801\tp__Proteobacteria\tc__Deltaproteobacteria\to__Oligoflexales\tf__Oligoflexaceae\tg__\ts__\n+OTU_3488\tp__Proteobacteria\tc__Betaproteobacteria\to__Neisseriales\tf__Neisseriaceae\tg__Rivicola\ts__\n+OTU_933\tp__Proteobacteria\tc__Deltaproteobacteria\to__GR-WP33-30\tf__\tg__\ts__\n+OTU_3824\tp__Lentisphaerae\tc__PBS-III-20\to__\tf__\tg__\ts__\n+OTU_777\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rickettsiales\tf__AKIW1012\tg__\ts__\n+OTU_3169\tp__TM6\tc__\to__\tf__\tg__\ts__\n+OTU_12385\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__[Eubacterium] coprostanoligenes group\ts__\n+OTU_1496\tp__Armatimonadetes\tc__\to__\tf__\tg__\ts__\n+OTU_11294\tp__Actinobacteria\tc__Acidimicrobiia\to__Acidimicrobiales\tf__Microthricaceae\tg__\ts__\n+OTU_1968\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Saprospiraceae\tg__Lewinella\ts__\n+OTU_8832\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rickettsiales\t\t\t\n+OTU_8652\tp__Proteobacteria\tc__Deltaproteobacteria\t\t\t\t\n+OTU_13621\tp__Chlorobi\tc__Chlorobia\to__Chlorobiales\tf__OPB56\tg__\ts__\n+OTU_3043\tp__Microgenomates\tc__\to__\tf__\tg__\ts__\n+OTU_10760\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\n+OTU_14173\tp__Bacteroidetes\tc__Bacteroidia\to__Bacteroidales\tf__Bacteroidaceae\tg__Bacteroides\ts__\n+OTU_10746\tp__Cyanobacteria\tc__Chloroplast\to__\tf__\tg__\ts__\n+OTU_284\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__uncultured\ts__\n+OTU_5049\tp__Saccharibacteria\tc__\to__\tf__\tg__\ts__\n+OTU_2397\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\n+OTU_2913\tp__Planctomycetes\tc__Planctomycetacia\to__Planctomycetales\tf__Planctomycetaceae\tg__uncultured\ts__\n+OTU_9512\tp__Bacteroidetes\t\t\t\t\t\n' 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| Binary file test-data/output_phyloseq.rds has changed |