Mercurial > repos > qfabrepo > metadegalaxy_phyloseq_abundance_factor
changeset 0:3856a1590a11 draft default tip
"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 |
| parents | |
| children | |
| files | phyloseq_abundance_factor.r phyloseq_abundance_factor.xml test-data/abundace_factor.html test-data/biom_out.html test-data/metadata.txt test-data/test.biom |
| diffstat | 6 files changed, 237 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyloseq_abundance_factor.r Mon Sep 14 08:02:08 2020 +0000 @@ -0,0 +1,91 @@ + +library('getopt') +suppressPackageStartupMessages(library('phyloseq')) +Sys.setenv("DISPLAY"=":1") + + +cmd_args <- commandArgs(TRUE) +options(warn=-1) +option_specification = matrix(c( + 'biomfile','b',2,'character', + 'metafile','m',2,'character', + 'xcolumn','x',2,'numeric', + 'lcolumn','l',2,'numeric', + 'factor1','f1',2,'numeric', + 'factor2','f2',1,'numeric', + '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) + + +pdffile <- gsub("[ ]+", "", paste(options$outdir,"/abundance.pdf")) +pngfile_abundance <- gsub("[ ]+", "", paste(options$outdir,"/abundance.png")) +htmlfile <- gsub("[ ]+", "", paste(options$htmlfile)) + + +###### To obtain the column name in metadata ################ +x.selectedColumn<-colnames(galaxy_map)[options$xcolumn] +l.selectedColumn<-colnames(galaxy_map)[options$lcolumn] +f1.selectedColumn<-colnames(galaxy_map)[options$factor1] + +factor.var <- f1.selectedColumn + +if(!is.null(options$factor2)){ +f2.selectedColumn<-colnames(galaxy_map)[options$factor2] +factor.var <- paste(f1.selectedColumn,f2.selectedColumn,sep="+") +} + + +# Produce PDF file +pdf(pdffile); +plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),fill=l.selectedColumn) +garbage<-dev.off(); + +#png('abundance_1.png') +bitmap(pngfile_abundance,"png16m") +plot_bar(AIP_galaxy,x=x.selectedColumn,facet_grid = paste('~', factor.var),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="abundance.pdf"><img src="abundance.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_factor.xml Mon Sep 14 08:02:08 2020 +0000 @@ -0,0 +1,108 @@ +<tool id="phyloseq_abundance" name="Phyloseq Abundance plot" version="1.22.3.3" hidden="false"> + <description>Phyloseq Abundance Plot with the factors of choice</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_factor.r' + #if str($factor.type) == "one": + --biomfile=$biom_input + --metafile=$metadata_input + --xcolumn="${xaxis_column}" + --lcolumn="${legend_column}" + --factor1="${factor.factor_column1}" + --outdir="$htmlfile.files_path" + --htmlfile='$htmlfile' + #else if str($factor.type) == "two": + --biomfile='$biom_input' + --metafile='$metadata_input' + --xcolumn="${xaxis_column}" + --lcolumn="${legend_column}" + --factor1="${factor.factor_column1}" + --factor2="${factor.factor_column2}" + --outdir="$htmlfile.files_path" + --htmlfile='$htmlfile' + #end if + ]]> </command> + + + <inputs> + + <param format="biom1" name="biom_input" type="data" label="BIOM file"/> + <param format="tabular" name="metadata_input" type="data" label="Metadata file"/> + <param name="xaxis_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used for X-axis"/> + <param name="legend_column" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as legend"/> + <conditional name="factor"> + <param name="type" type="select" label="Is this one factor or two factor"> + <option value="one">1</option> + <option value="two">2</option> + </param> + <when value="one"> + <param name="factor_column1" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 1"/> + </when> + <when value="two"> + <param name="factor_column1" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 1"/> + <param name="factor_column2" type="data_column" data_ref="metadata_input" use_header_names="TRUE" label="Column used as factor 2"/> + </when> + </conditional> + + </inputs> + + <outputs> + <data format="html" name="htmlfile" label="${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="3" /> + <param name="type" value="1" /> + <param name="factor_column1" value="4"/> + <output name="htmlfile" ftype="html" file="abundace_factor.html" /> + </test> + </tests> + + <help> +**What it does** +Creates an abundance 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. +- **Is this one factor or two factor** - This is the facet_grid feature of phyloseq's plot_bar to allow plotting with two factors (e.g, facet_grid=~protein + allergy) +- **Column used as factor 1** - select the first factor for facet_grid feature from the metadata file + +.. _BIOM: http://biom-format.org/ + +----- + +========= +Resources +========= + +**Wrapper Authors** + +QFAB Bioinformatics (support@qfab.org) + + </help> + <citations> + <citation type="doi">10.18129/B9.bioc.phyloseq</citation> + <citation type="doi">doi:10.1186/2047-217X-1-7</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundace_factor.html Mon Sep 14 08:02:08 2020 +0000 @@ -0,0 +1,9 @@ +<html><body> +<table align="center"> +<tr> +<td valign="middle" style="vertical-align:middle;"> +<a href="abundance.pdf"><img src="abundance.png"/></a> +</td> +</tr> +</table> +</html></body>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biom_out.html Mon Sep 14 08:02:08 2020 +0000 @@ -0,0 +1,9 @@ +<html><body> +<table align="center"> +<tr> +<td valign="middle" style="vertical-align:middle;"> +<a href="pdffile.pdf"><img src="nmds.png" width="800" height="800"/></a> +</td> +</tr> +</table> +</html></body>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata.txt Mon Sep 14 08:02:08 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 08:02:08 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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