Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_abundance_taxonomy

annotate phyloseq_abundance_taxonomy.r @ 0:b2fafdd3533d draft default tip

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:07:43 +0000
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
qfabrepo
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diff changeset
1 library('getopt')
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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2 suppressPackageStartupMessages(library('phyloseq'))
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3 Sys.setenv("DISPLAY"=":1")
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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5 options(warn=-1)
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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6 option_specification = matrix(c(
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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7 'biomfile','b',2,'character',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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8 'metafile','m',2,'character',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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9 'xcolumn','x',2,'numeric',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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10 'lcolumn','l',2,'numeric',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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11 'taxonomy','t',2,'character',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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12 'outdir','o',2,'character',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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13 'htmlfile','h',2,'character'
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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14 ),byrow=TRUE,ncol=4);
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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17 options <- getopt(option_specification);
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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18 options(bitmapType="cairo")
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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21 if (!is.null(options$outdir)) {
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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22 # Create the directory
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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23 dir.create(options$outdir,FALSE)
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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24 }
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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27 galaxy_biom <- import_biom(options$biomfile)
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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28 galaxy_map <- import_qiime_sample_data(options$metafile)
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
qfabrepo
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29 tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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30 tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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32 number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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34 if( number.of.tax.rank == 7){
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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35 colnames(tax_table(galaxy_biom)) <- tax_col_norm
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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36 }else{
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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37 colnames(tax_table(galaxy_biom)) <- tax_col_extra
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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38 }
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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41 AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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44 x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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45 l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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47 tax.selected<-options$taxonomy
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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48
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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49 pdffile <- gsub("[ ]+", "", paste(options$outdir,"/kingdom.pdf"))
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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50 pngfile_kingdom <- gsub("[ ]+", "", paste(options$outdir,"/kingdom.png"))
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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51 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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53
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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54 # Produce PDF file
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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55 pdf(pdffile);
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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56 plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', tax.selected),fill=l.selectedColumn)
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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57 garbage<-dev.off();
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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58
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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59 #png('kingdom.png')
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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60 bitmap(pngfile_kingdom,"png16m")
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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61 plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', tax.selected),fill=l.selectedColumn)
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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62 garbage<-dev.off()
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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63
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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64 # Produce the HTML file
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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65 htmlfile_handle <- file(htmlfile)
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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66 html_output = c('<html><body>',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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67 '<table align="center">',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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68 '<tr>',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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69 '<td valign="middle" style="vertical-align:middle;">',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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70 '<a href="kingdom.pdf"><img src="kingdom.png"/></a>',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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71 '</td>',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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72 '</tr>',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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73 '</table>',
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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74 '</html></body>');
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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75 writeLines(html_output, htmlfile_handle);
b2fafdd3533d "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_taxonomy commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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76 close(htmlfile_handle);