Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_richness
annotate phyloseq_richness.r @ 1:e0225f3e8ef6 draft default tip
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit ee9929d341d4f23237db43fcdd688b99366a8e48"
author | qfabrepo |
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date | Tue, 15 Sep 2020 01:08:50 +0000 |
parents | 0ab4501d805b |
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rev | line source |
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0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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1 library('getopt') |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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2 suppressPackageStartupMessages(library('phyloseq')) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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3 Sys.setenv("DISPLAY"=":1") |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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4 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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5 options(warn=-1) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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6 option_specification = matrix(c( |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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7 'biomfile','b',2,'character', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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8 'metafile','m',2,'character', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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9 'xcolumn','x',2,'numeric', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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10 'lcolumn','l',2,'numeric', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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11 'outdir','o',2,'character', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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12 'htmlfile','h',2,'character' |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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13 ),byrow=TRUE,ncol=4); |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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14 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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15 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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16 options <- getopt(option_specification); |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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17 options(bitmapType="cairo") |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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18 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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19 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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20 if (!is.null(options$outdir)) { |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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21 # Create the directory |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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22 dir.create(options$outdir,FALSE) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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23 } |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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24 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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25 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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26 galaxy_biom <- import_biom(options$biomfile) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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27 galaxy_map <- import_qiime_sample_data(options$metafile) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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28 tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species") |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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29 tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species") |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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30 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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31 number.of.tax.rank<-length(colnames(tax_table(galaxy_biom))) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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32 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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33 if( number.of.tax.rank == 7){ |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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34 colnames(tax_table(galaxy_biom)) <- tax_col_norm |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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35 }else{ |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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36 colnames(tax_table(galaxy_biom)) <- tax_col_extra |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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37 } |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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38 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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39 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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40 AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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41 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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42 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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43 x.selectedColumn<-colnames(galaxy_map)[options$xcolumn] |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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44 l.selectedColumn<-colnames(galaxy_map)[options$lcolumn] |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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45 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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46 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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47 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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48 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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49 pdffile <- gsub("[ ]+", "", paste(options$outdir,"/pdffile.pdf")) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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50 pngfile_richness <- gsub("[ ]+", "", paste(options$outdir,"/richness.png")) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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51 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile)) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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52 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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53 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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54 # Produce PDF file |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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55 pdf(pdffile); |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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56 plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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57 garbage<-dev.off(); |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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58 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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59 #png('richness.png') |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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60 bitmap(pngfile_richness,"png16m") |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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61 plot_richness(AIP_galaxy,measures=c("Observed"),color=l.selectedColumn,x=x.selectedColumn) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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62 garbage<-dev.off() |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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63 |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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64 # Produce the HTML file |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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65 htmlfile_handle <- file(htmlfile) |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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66 html_output = c('<html><body>', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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67 '<table align="center">', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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68 '<tr>', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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69 '<td valign="middle" style="vertical-align:middle;">', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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70 '<a href="pdffile.pdf"><img src="richness.png"/></a>', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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71 '</td>', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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72 '</tr>', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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73 '</table>', |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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74 '</html></body>'); |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
parents:
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75 writeLines(html_output, htmlfile_handle); |
0ab4501d805b
"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/phyloseq_richness commit a8245efa0d80103939285565948beaf8dfb88a73"
qfabrepo
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76 close(htmlfile_handle); |