Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_net

annotate phyloseq_net.r @ 0:af6d9ad14a0f draft

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:13:43 +0000
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af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
qfabrepo
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diff changeset
1 library('getopt')
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
qfabrepo
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2 library('data.table')
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3 suppressPackageStartupMessages(library('phyloseq'))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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4 suppressPackageStartupMessages(library('DESeq2'))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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6 Sys.setenv("DISPLAY"=":1")
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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7
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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8 options(warn= -1)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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9 option_specification = matrix(c(
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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10 'infile','i',2,'character',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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11 'metafile','m',2,'character',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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12 'biom','b',2,'character',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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13 'obsfile','o',2,'character',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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14 'norm','n',2,'logical',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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15 'xcolumn','x',2,'numeric',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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16 'lcolumn','l',2,'numeric',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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17 'outdir','d',2,'character',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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18 'htmlfile','h',2,'character'
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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19 ),byrow=TRUE,ncol=4);
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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22 options <- getopt(option_specification)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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23 options(bitmapType="cairo")
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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25 matrix.format<-function(x) {
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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26 m<-as.matrix(x[,-1])
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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27 rownames(m)<-x[,1]
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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28 m
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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29 }
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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32 gm_mean = function(x, na.rm=TRUE){ exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))}
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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34
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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35 tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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36 tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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37
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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38 tax_col_norm_otu <- c("OTUID","Kingdom","Phylum","Class","Order","Family","Genus","Species")
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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39 tax_col_extra_otu <- c("OTUID","None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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40
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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41 if (!is.null(options$outdir)) {
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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42 # Create the directory
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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43 dir.create(options$outdir,FALSE)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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44 }
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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45
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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46 is.biom<-options$biom
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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47
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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48
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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49 pdffile <- gsub("[ ]+", "", paste(options$outdir,"/pdffile.pdf"))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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50 pngfile_net <- gsub("[ ]+", "", paste(options$outdir,"/net.png"))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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51 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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52
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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53 if(is.biom=="set_biom"){
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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54
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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55 galaxy_biom <- import_biom(options$infile)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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56 galaxy_map <- import_qiime_sample_data(options$metafile)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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57
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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58 number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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59
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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60 if(number.of.tax.rank == 7){
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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61 colnames(tax_table(galaxy_biom)) <- tax_col_norm
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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62 } else {
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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63 colnames(tax_table(galaxy_biom)) <- tax_col_extra
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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64 }
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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65
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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66 physeq_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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67
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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68 } else {
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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69
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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70 count.table<-read.table(options$infile,header=T,sep="\t",comment.char="",stringsAsFactors = F)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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71 meta.table<-read.table(options$metafile,header=T,sep="\t",comment.char="",stringsAsFactors = F)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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72 tax.table<-read.table(options$obsfile,header=T,sep="\t",comment.char="",stringsAsFactors = F)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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73
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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74
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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75 colnames(count.table)<-gsub("^X","",colnames(count.table))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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76 colnames(meta.table)<-gsub("^X.","",colnames(meta.table))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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77 colnames(tax.table)<-gsub("^X.","",colnames(tax.table))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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78
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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79 count.table.formatted<-matrix.format(count.table)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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80 OTU<-otu_table(count.table.formatted,taxa_are_rows = TRUE)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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81
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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82 tax.table.new<-as.data.frame(cbind(tax.table[,1],t(as.data.table(strsplit(tax.table[,2],";")))))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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83
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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84
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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85 if(length(colnames(tax.table.new)) != length(tax_col_extra_otu)){
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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86 colnames(tax.table.new)<-tax_col_norm_otu
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
qfabrepo
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87 }else{
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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88 colnames(tax.table.new)<-tax_col_extra_otu
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
qfabrepo
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89 }
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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90
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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91 tax.table.formatted<-matrix.format(tax.table.new)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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92
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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93 TAX<-tax_table(tax.table.formatted)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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94
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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95 physeq_galaxy <- phyloseq(OTU, TAX)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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96
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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97
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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98 galaxy_map<-meta.table
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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99
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
qfabrepo
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100 rownames(galaxy_map)<-meta.table[,1]
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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101
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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102 sampledata<-sample_data(as.data.frame(galaxy_map,row.names=sample_names(galaxy_map),stringsAsFactos=F))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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103
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
qfabrepo
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104 sample_data(physeq_galaxy)<-sampledata
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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105
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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106 }
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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107
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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108
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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109 x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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110 l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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111
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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112 ### normalisation
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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113 if(is.null(options$norm) || options$norm =="false"){
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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114 suppressMessages(raw.count.deseq2.obj<-phyloseq_to_deseq2(physeq_galaxy,as.formula(paste('~',x.selectedColumn,sep=""))))
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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115 geoMeans = apply(counts(raw.count.deseq2.obj), 1, gm_mean)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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116
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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117 deseq.obj = estimateSizeFactors(raw.count.deseq2.obj, geoMeans = geoMeans)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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118 deseq.obj.norm<-otu_table(as.matrix(counts(deseq.obj,normalized=T)),taxa_are_rows=TRUE)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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119
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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120 otu_table(physeq_galaxy)<-deseq.obj.norm
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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121 }
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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122
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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123
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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124 # Produce PDF file
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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125
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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126 pdf(pdffile);
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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127 plot_net(physeq_galaxy,point_label=x.selectedColumn,color=l.selectedColumn)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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128 garbage<-dev.off();
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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129
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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130 #Cairo(pngfile_net, type="png", bg="white",pointsize=12,dpi=100,units="in",width=6,height=6)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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131 png(pngfile_net,units="in",width=6,height=6,pointsize=12,res=100,bg="white")
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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132 plot_net(physeq_galaxy,point_label=x.selectedColumn,color=l.selectedColumn)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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133 garbage<-dev.off()
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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134
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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135 # Produce the HTML file
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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136 htmlfile_handle <- file(htmlfile)
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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137 html_output = c('<html><body>',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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138 '<table align="center">',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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139 '<tr>',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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140 '<td valign="middle" style="vertical-align:middle;">',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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141 '<a href="pdffile.pdf"><img src="net.png"/></a>',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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142 '</td>',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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143 '</tr>',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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144 '</table>',
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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145 '</html></body>');
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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146 writeLines(html_output, htmlfile_handle);
af6d9ad14a0f "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_net commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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147 close(htmlfile_handle);