Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_abundance_taxonomy
changeset 0:b2fafdd3533d draft default tip
"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 |
| parents | |
| children | |
| files | phyloseq_abundance_taxonomy.r phyloseq_abundance_taxonomy.xml test-data/GP.biom test-data/biom_out.html test-data/metadata.txt test-data/test.biom |
| diffstat | 6 files changed, 192 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_abundance_taxonomy.r Mon Sep 14 08:07:43 2020 +0000 @@ -0,0 +1,76 @@ +library('getopt') +suppressPackageStartupMessages(library('phyloseq')) +Sys.setenv("DISPLAY"=":1") + +options(warn=-1) +option_specification = matrix(c( + 'biomfile','b',2,'character', + 'metafile','m',2,'character', + 'xcolumn','x',2,'numeric', + 'lcolumn','l',2,'numeric', + 'taxonomy','t',2,'character', + 'outdir','o',2,'character', + 'htmlfile','h',2,'character' +),byrow=TRUE,ncol=4); + + +options <- getopt(option_specification); +options(bitmapType="cairo") + + +if (!is.null(options$outdir)) { + # Create the directory + dir.create(options$outdir,FALSE) +} + + +galaxy_biom <- import_biom(options$biomfile) +galaxy_map <- import_qiime_sample_data(options$metafile) +tax_col_norm <- c("Kingdom","Phylum","Class","Order","Family","Genus","Species") +tax_col_extra <- c("None","Kingdom","Phylum","Class","Order","Family","Genus","Species") + +number.of.tax.rank<-length(colnames(tax_table(galaxy_biom))) + +if( number.of.tax.rank == 7){ +colnames(tax_table(galaxy_biom)) <- tax_col_norm +}else{ +colnames(tax_table(galaxy_biom)) <- tax_col_extra +} + + +AIP_galaxy <- merge_phyloseq(galaxy_biom,galaxy_map) + + +x.selectedColumn<-colnames(galaxy_map)[options$xcolumn] +l.selectedColumn<-colnames(galaxy_map)[options$lcolumn] + +tax.selected<-options$taxonomy + +pdffile <- gsub("[ ]+", "", paste(options$outdir,"/kingdom.pdf")) +pngfile_kingdom <- gsub("[ ]+", "", paste(options$outdir,"/kingdom.png")) +htmlfile <- gsub("[ ]+", "", paste(options$htmlfile)) + + +# Produce PDF file +pdf(pdffile); +plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', tax.selected),fill=l.selectedColumn) +garbage<-dev.off(); + +#png('kingdom.png') +bitmap(pngfile_kingdom,"png16m") +plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', tax.selected),fill=l.selectedColumn) +garbage<-dev.off() + +# Produce the HTML file +htmlfile_handle <- file(htmlfile) +html_output = c('<html><body>', + '<table align="center">', + '<tr>', + '<td valign="middle" style="vertical-align:middle;">', + '<a href="kingdom.pdf"><img src="kingdom.png"/></a>', + '</td>', + '</tr>', + '</table>', + '</html></body>'); +writeLines(html_output, htmlfile_handle); +close(htmlfile_handle);
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_abundance_taxonomy.xml Mon Sep 14 08:07:43 2020 +0000 @@ -0,0 +1,86 @@ +<tool id="phyloseq_taxonomy" name="Phyloseq Abundance Taxonomy" version="1.22.3.3" hidden="false"> + <description>Phyloseq Abundance Plot on Taxonomy level</description> + <requirements> + <requirement type="package" version="3.4.1">r-base</requirement> + <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="9.18">ghostscript</requirement> + </requirements> + <version_command><![CDATA[ + echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + <command detect_errors="exit_code"><![CDATA[ + Rscript '${__tool_directory__}/phyloseq_abundance_taxonomy.r' + --biomfile='$biom_input' + --metafile='$metadata_input' + --xcolumn="${xaxis_column}" + --lcolumn="${legend_column}" + --taxonomy="${taxonomy_rank}" + --outdir="$htmlfile.files_path" + --htmlfile='$htmlfile' + ]]></command> + + <inputs> + <param format="biom1" name="biom_input" type="data" label="BIOM file"/> + <param format="tabular" name="metadata_input" type="data" label="Metadata file"/> + <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/> + <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/> + <param name="taxonomy_rank" type="select" display="radio" label="Select a taxonomy rank"> + <option value="Kingdom" selected="true">Kingdom</option> + <option value="Phylum">Phylum</option> + <option value="Class">Class</option> + <option value="Order">Order</option> + <option value="Family">Family</option> + <option value="Genus">Genus</option> + <option value="Species">Species</option> + </param> + </inputs> + + <outputs> + <data format="html" name="htmlfile" label="${tool.name}.html"/> + </outputs> + + <tests> + <test> + <param name="biom_input" value="test.biom" ftype="biom1" /> + <param name="metadata_input" value="metadata.txt" /> + <param name="xaxis_column" value="5" /> + <param name="legend_column" value="4" /> + <param name="taxonomy_rank" value="Phylum" /> + <output name="htmlfile" ftype="html" file="biom_out.html" /> + </test> + </tests> + <help> +**What it does** +Creates an abundance with taxonomy barplot using an R package called phyloseq_. + +.. _phyloseq: https://joey711.github.io/phyloseq/plot_bar-examples.html + +----- + +**Input** + + +- **BIOM file** - this is a BIOM_ file format +- **Metadata file** - this is a metadata file of the experiment design +- **Column used for X-axis** - The horizontal x-axis display on the barplot. +- **Column used as legend** - select a group from the metadata to fill color to represent the group it belongs to. +- **Select a taxonomy rank** - This is a taxonomy selection. + + +.. _BIOM: http://biom-format.org/ + +----- + +========= +Resources +========= + +**Wrapper Authors** +QFAB Bioinformatics (support@qfab.org) + + </help> + <citations> + <citation type="doi">10.18129/B9.bioc.phyloseq</citation> + </citations> +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biom_out.html Mon Sep 14 08:07:43 2020 +0000 @@ -0,0 +1,9 @@ +<html><body> +<table align="center"> +<tr> +<td valign="middle" style="vertical-align:middle;"> +<a href="kingdom.pdf"><img src="kingdom.png"/></a> +</td> +</tr> +</table> +</html></body>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata.txt Mon Sep 14 08:07:43 2020 +0000 @@ -0,0 +1,19 @@ +#SampleID dpw time Food Replicate_Group +F3D0 0 Early None Group1 +F3D1 1 Early None Group1 +F3D2 2 Early None Group1 +F3D3 3 Early Cheddar Group2 +F3D5 5 Early Cheddar Group2 +F3D6 6 Early Cheddar Group2 +F3D7 7 Early Swiss Group3 +F3D8 8 Early Swiss Group3 +F3D9 9 Early Swiss Group3 +F3D141 141 Late Cheddar Group4 +F3D142 142 Late Cheddar Group4 +F3D143 143 Late Cheddar Group4 +F3D144 144 Late None Group5 +F3D145 145 Late None Group5 +F3D146 146 Late None Group5 +F3D147 147 Late Swiss Group6 +F3D148 148 Late Swiss Group6 +F3D149 149 Late Swiss Group6
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.biom Mon Sep 14 08:07:43 2020 +0000 @@ -0,0 +1,1 @@ +{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.5","date": "2017-09-08T01:49:15.647451","type": "OTU table","matrix_element_type": "float","shape": [5339, 18],"data": 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