| Previous changeset 0:4bcb464fb3f3 (2022-04-04) Next changeset 2:f8c8c943245f (2023-12-18) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283" |
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modified:
macros.xml test-data/generate.R |
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added:
test-data/AalborgWWTPs.2010.rds test-data/AalborgWWTPs.2011.rds test-data/AalborgWWTPs.tax.tsv |
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| diff -r 4bcb464fb3f3 -r 354d645455cd macros.xml --- a/macros.xml Mon Apr 04 10:24:03 2022 +0000 +++ b/macros.xml Thu Apr 07 14:05:48 2022 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.7.17</token> + <token name="@TOOL_VERSION@">2.7.22</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">22.01</token> <xml name="header"> @@ -22,8 +22,8 @@ </citations> </xml> - <xml name="rds_input_macro"> - <param argument="data" type="data" format="ampvis2" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/> + <xml name="rds_input_macro" token_multiple="false"> + <param argument="data" type="data" format="ampvis2" multiple="@MULTIPLE@" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/> </xml> <xml name="rds_metadata_input_macro" token_metadata_optional="true"> |
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| diff -r 4bcb464fb3f3 -r 354d645455cd test-data/AalborgWWTPs.2010.rds |
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| Binary file test-data/AalborgWWTPs.2010.rds has changed |
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| diff -r 4bcb464fb3f3 -r 354d645455cd test-data/AalborgWWTPs.2011.rds |
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| Binary file test-data/AalborgWWTPs.2011.rds has changed |
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| diff -r 4bcb464fb3f3 -r 354d645455cd test-data/AalborgWWTPs.tax.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AalborgWWTPs.tax.tsv Thu Apr 07 14:05:48 2022 +0000 |
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| b'@@ -0,0 +1,201 @@\n+Kingdom\tPhylum\tClass\tOrder\tFamily\tGenus\tSpecies\tOTU\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnospiraceae\tg__Acetitomaculum\ts__\tOTU_8735\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminococcaceae UCG-005\ts__\tOTU_13382\n+k__Bacteria\tp__Bacteroidetes\tc__Cytophagia\to__Cytophagales\tf__Cytophagaceae\tg__Dyadobacter\ts__\tOTU_5516\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Nitrosomonadales\tf__Nitrosomonadaceae\tg__Nitrosomonas\ts__\tOTU_8315\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Intrasporangiaceae\tg__Tetrasphaera\ts__\tOTU_10522\n+k__Bacteria\tp__Proteobacteria\tc__Gammaproteobacteria\to__Xanthomonadales\tf__Xanthomonadaceae\t\t\tOTU_11040\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Desulfobacterales\tf__Desulfobacteraceae\tg__Desulforegula\ts__\tOTU_7263\n+k__Bacteria\tp__Firmicutes\tc__Bacilli\to__Bacillales\tf__Planococcaceae\tg__Rummeliibacillus\ts__\tOTU_13379\n+k__Bacteria\tp__Hydrogenedentes\tc__\to__\tf__\tg__\ts__\tOTU_1418\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Lachnospiraceae\tg__Fusicatenibacter\ts__\tOTU_556\n+k__Bacteria\tp__Parcubacteria\tc__\to__\tf__\tg__\ts__\tOTU_6869\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminiclostridium 1\ts__\tOTU_10171\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Dermatophilaceae\tg__uncultured\ts__\tOTU_2830\n+k__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__AKYH767\tg__\ts__\tOTU_4232\n+k__Bacteria\tp__Planctomycetes\tc__Planctomycetacia\to__Planctomycetales\tf__Planctomycetaceae\t\t\tOTU_12831\n+k__Bacteria\tp__Acidobacteria\tc__Holophagae\to__Holophagales\tf__Holophagaceae\t\t\tOTU_613\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Propionibacteriales\tf__Propionibacteriaceae\tg__Brooklawnia\ts__\tOTU_3625\n+k__Bacteria\tp__Chloroflexi\tc__Chloroflexia\to__Chloroflexales\tf__Roseiflexaceae\tg__\ts__\tOTU_3605\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__PeM15\tf__PeM15\tg__\ts__\tOTU_11148\n+k__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__uncultured\ts__\tOTU_656\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Rhodocyclales\tf__Rhodocyclaceae\tg__Sulfuritalea\ts__\tOTU_4382\n+k__Bacteria\t\t\t\t\t\t\tOTU_3834\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\t\t\t\tOTU_13127\n+k__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\t\t\t\tOTU_4528\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Myxococcales\tf__Blfdi19\tg__\ts__\tOTU_4485\n+k__Bacteria\tp__Firmicutes\tc__Bacilli\to__Lactobacillales\tf__Lactobacillaceae\tg__Lactobacillus\ts__\tOTU_12265\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\tOTU_11820\n+k__Bacteria\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\tOTU_4093\n+k__Bacteria\tp__Bacteroidetes\tc__Flavobacteriia\to__Flavobacteriales\tf__Flavobacteriaceae\tg__Flavobacterium\ts__\tOTU_8360\n+k__Bacteria\tp__Firmicutes\tc__Negativicutes\to__Selenomonadales\tf__Veillonellaceae\t\t\tOTU_15123\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Desulfobacterales\tf__Desulfobacteraceae\t\t\tOTU_11928\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Acetobacteraceae\tg__Acidicaldus\ts__\tOTU_11334\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Myxococcales\tf__mle1-27\tg__\ts__\tOTU_4511\n+k__Bacteria\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\tOTU_3265\n+k__Bacteria\tp__Actinobacteria\t\t\t\t\t\tOTU_2991\n+k__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__Candidatus Defluviifilum\ts__\tOTU_522\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Nitrosomonadales\tf__Nitrosomonadaceae\tg__Nitrosomonas\ts__\tOTU_11832\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminococcaceae UCG-010\ts__\tOTU_6358\n+k__Bacteria\tp__Saccharibacteria\tc__Unknown Class\to__Unknown Order\tf__SBR2060\tg__SBR2113\ts__\tOTU_3611\n+k'..b'\to__Clostridiales\tf__Christensenellaceae\tg__Christensenellaceae R-7 group\ts__\tOTU_8245\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\tOTU_10847\n+k__Bacteria\tp__Acidobacteria\tc__Holophagae\to__Holophagales\tf__Holophagaceae\t\t\tOTU_1151\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Intrasporangiaceae\tg__Fodinibacter\ts__\tOTU_1998\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Rhodospirillaceae\tg__Defluviicoccus\ts__cluster I\tOTU_10321\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Burkholderiales\tf__Comamonadaceae\tg__Acidovorax\ts__\tOTU_4721\n+k__Bacteria\tp__Verrucomicrobia\tc__OPB35 soil group\to__\tf__\tg__\ts__\tOTU_6237\n+k__Bacteria\tp__Saccharibacteria\tc__Unknown Class\to__FW73\t\t\t\tOTU_1972\n+k__Bacteria\tp__Elusimicrobia\tc__Elusimicrobia\to__Lineage IIb\tf__\tg__\ts__\tOTU_11364\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Micrococcales\tf__Beutenbergiaceae\tg__Salana\ts__\tOTU_1816\n+k__Bacteria\tp__Actinobacteria\tc__Actinobacteria\to__Propionibacteriales\tf__Propionibacteriaceae\tg__Propionimicrobium\ts__\tOTU_14842\n+k__Bacteria\tp__Fusobacteria\tc__Fusobacteriia\to__Fusobacteriales\tf__Leptotrichiaceae\tg__uncultured\ts__\tOTU_6533\n+k__Bacteria\tp__Tenericutes\tc__Mollicutes\to__Mollicutes RF9\tf__\tg__\ts__\tOTU_8887\n+k__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__Litorilinea\ts__\tOTU_12690\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Clostridiaceae 1\tg__Proteiniclasticum\ts__\tOTU_3097\n+k__Bacteria\tp__Firmicutes\tc__Erysipelotrichia\to__Erysipelotrichales\tf__Erysipelotrichaceae\tg__Faecalitalea\ts__\tOTU_3257\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rhodospirillales\tf__Acetobacteraceae\tg__uncultured\ts__\tOTU_3161\n+k__Bacteria\tp__Actinobacteria\tc__Thermoleophilia\to__Solirubrobacterales\tf__480-2\tg__\ts__\tOTU_11903\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__Ruminiclostridium 5\ts__\tOTU_7508\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Oligoflexales\tf__\tg__\ts__\tOTU_10969\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__Oligoflexales\tf__Oligoflexaceae\tg__\ts__\tOTU_1801\n+k__Bacteria\tp__Proteobacteria\tc__Betaproteobacteria\to__Neisseriales\tf__Neisseriaceae\tg__Rivicola\ts__\tOTU_3488\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\to__GR-WP33-30\tf__\tg__\ts__\tOTU_933\n+k__Bacteria\tp__Lentisphaerae\tc__PBS-III-20\to__\tf__\tg__\ts__\tOTU_3824\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rickettsiales\tf__AKIW1012\tg__\ts__\tOTU_777\n+k__Bacteria\tp__TM6\tc__\to__\tf__\tg__\ts__\tOTU_3169\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\tg__[Eubacterium] coprostanoligenes group\ts__\tOTU_12385\n+k__Bacteria\tp__Armatimonadetes\tc__\to__\tf__\tg__\ts__\tOTU_1496\n+k__Bacteria\tp__Actinobacteria\tc__Acidimicrobiia\to__Acidimicrobiales\tf__Microthricaceae\tg__\ts__\tOTU_11294\n+k__Bacteria\tp__Bacteroidetes\tc__Sphingobacteriia\to__Sphingobacteriales\tf__Saprospiraceae\tg__Lewinella\ts__\tOTU_1968\n+k__Bacteria\tp__Proteobacteria\tc__Alphaproteobacteria\to__Rickettsiales\t\t\t\tOTU_8832\n+k__Bacteria\tp__Proteobacteria\tc__Deltaproteobacteria\t\t\t\t\tOTU_8652\n+k__Bacteria\tp__Chlorobi\tc__Chlorobia\to__Chlorobiales\tf__OPB56\tg__\ts__\tOTU_13621\n+k__Bacteria\tp__Microgenomates\tc__\to__\tf__\tg__\ts__\tOTU_3043\n+k__Bacteria\tp__Firmicutes\tc__Clostridia\to__Clostridiales\tf__Ruminococcaceae\t\t\tOTU_10760\n+k__Bacteria\tp__Bacteroidetes\tc__Bacteroidia\to__Bacteroidales\tf__Bacteroidaceae\tg__Bacteroides\ts__\tOTU_14173\n+k__Bacteria\tp__Cyanobacteria\tc__Chloroplast\to__\tf__\tg__\ts__\tOTU_10746\n+k__Bacteria\tp__Chloroflexi\tc__Caldilineae\to__Caldilineales\tf__Caldilineaceae\tg__uncultured\ts__\tOTU_284\n+k__Bacteria\tp__Saccharibacteria\tc__\to__\tf__\tg__\ts__\tOTU_5049\n+k__Bacteria\tp__Chloroflexi\tc__Anaerolineae\to__Anaerolineales\tf__Anaerolineaceae\tg__uncultured\ts__\tOTU_2397\n+k__Bacteria\tp__Planctomycetes\tc__Planctomycetacia\to__Planctomycetales\tf__Planctomycetaceae\tg__uncultured\ts__\tOTU_2913\n+k__Bacteria\tp__Bacteroidetes\t\t\t\t\t\tOTU_9512\n' 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| diff -r 4bcb464fb3f3 -r 354d645455cd test-data/generate.R --- a/test-data/generate.R Mon Apr 04 10:24:03 2022 +0000 +++ b/test-data/generate.R Thu Apr 07 14:05:48 2022 +0000 |
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| @@ -8,3 +8,19 @@ amp_export_otutable(aalborgwwtps, "AalborgWWTPs.otu") write.table(aalborgwwtps$tax, file = "AalborgWWTPs.tax", quote = F, sep = "\t", row.names = F) write.table(aalborgwwtps$metadata, file = "AalborgWWTPs.tsv", quote = F, sep = "\t") + +# construct data for merge_ampvis2 +t <- amp_load(otutable = "AalborgWWTPs.otu.csv", metadata = "AalborgWWTPs.tsv", taxonomy = "AalborgWWTPs.tax.tsv", fasta = "AalborgWWTPs.fa", tree = "AalborgWWTPs.nwk") +d_2010 <- amp_subset_samples(t, Period %in% "2010") +# 60 samples and 109 OTUs have been filtered +# Before: 67 samples and 200 OTUs +# After: 7 samples and 91 OTUs +d_2011 <- amp_subset_samples(t, Period %in% "2011") +# 61 samples and 94 OTUs have been filtered +# Before: 67 samples and 200 OTUs +# After: 6 samples and 106 OTUs + +saveRDS(d_2010, "AalborgWWTPs.2010.rds") +saveRDS(d_2011, "AalborgWWTPs.2011.rds") + +# => merging should give 13 samples |