Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_abundance_factor

annotate phyloseq_abundance_factor.r @ 0:3856a1590a11 draft default tip

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"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
author qfabrepo
date Mon, 14 Sep 2020 08:02:08 +0000
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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2 library('getopt')
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3 suppressPackageStartupMessages(library('phyloseq'))
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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4 Sys.setenv("DISPLAY"=":1")
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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7 cmd_args <- commandArgs(TRUE)
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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8 options(warn=-1)
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9 option_specification = matrix(c(
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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10 'biomfile','b',2,'character',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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11 'metafile','m',2,'character',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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12 'xcolumn','x',2,'numeric',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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13 'lcolumn','l',2,'numeric',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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14 'factor1','f1',2,'numeric',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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15 'factor2','f2',1,'numeric',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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16 'outdir','o',2,'character',
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17 'htmlfile','h',2,'character'
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18 ),byrow=TRUE,ncol=4);
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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21 options <- getopt(option_specification);
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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22 options(bitmapType="cairo")
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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26 if (!is.null(options$outdir)) {
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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27 # Create the directory
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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28 dir.create(options$outdir,FALSE)
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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29 }
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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32 galaxy_biom <- import_biom(options$biomfile)
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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33 galaxy_map <- import_qiime_sample_data(options$metafile)
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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36 tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species")
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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37 tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species")
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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39 number.of.tax.rank<-length(colnames(tax_table(galaxy_biom)))
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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41 if( number.of.tax.rank == 7){
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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42 colnames(tax_table(galaxy_biom)) <- tax_col_norm
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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43 }else{
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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44 colnames(tax_table(galaxy_biom)) <- tax_col_extra
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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45 }
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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48 AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map)
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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51 pdffile <- gsub("[ ]+", "", paste(options$outdir,"/abundance.pdf"))
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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52 pngfile_abundance <- gsub("[ ]+", "", paste(options$outdir,"/abundance.png"))
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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53 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
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56 ###### To obtain the column name in metadata ################
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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57 x.selectedColumn<-colnames(galaxy_map)[options$xcolumn]
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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58 l.selectedColumn<-colnames(galaxy_map)[options$lcolumn]
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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59 f1.selectedColumn<-colnames(galaxy_map)[options$factor1]
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61 factor.var <- f1.selectedColumn
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63 if(!is.null(options$factor2)){
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64 f2.selectedColumn<-colnames(galaxy_map)[options$factor2]
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65 factor.var <- paste(f1.selectedColumn,f2.selectedColumn,sep="+")
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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66 }
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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69 # Produce PDF file
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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70 pdf(pdffile);
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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71 plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),fill=l.selectedColumn)
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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72 garbage<-dev.off();
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3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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74 #png('abundance_1.png')
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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75 bitmap(pngfile_abundance,"png16m")
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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76 plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),fill=l.selectedColumn)
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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77 garbage<-dev.off()
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78
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79 # Produce the HTML file
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80 htmlfile_handle <- file(htmlfile)
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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81 html_output = c('<html><body>',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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82 '<table align="center">',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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83 '<tr>',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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84 '<td valign="middle" style="vertical-align:middle;">',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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85 '<a href="abundance.pdf"><img src="abundance.png"/></a>',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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86 '</td>',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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87 '</tr>',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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88 '</table>',
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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89 '</html></body>');
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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90 writeLines(html_output, htmlfile_handle);
3856a1590a11 "planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_abundance_factor commit 8bd68662b72404f6291e9628327dcb109b5fa55e"
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91 close(htmlfile_handle);