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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_grouped_barplot commit c6ba903395dc6d41cb318c7d95a2d9cf3ca65313-dirty |
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plot_grouped_barplot.R plot_grouped_barplot.xml static/images/output.pdf static/images/output.png test-data/input_file.txt test-data/output_file.pdf tool_dependencies.xml |
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| diff -r 000000000000 -r 6c9aac0d6ca2 plot_grouped_barplot.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_grouped_barplot.R Mon Apr 18 10:08:25 2016 -0400 |
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| @@ -0,0 +1,87 @@ +library('getopt') + +option_specification = matrix(c( + 'input_file', 'i', 2, 'character', + 'output_pdf_file', 'p', 2, 'character', + 'output_png_file', 'o', 2, 'character', + 'output_svg_file', 's', 2, 'character', + 'data_columns', 'd', 2, 'list', + 'names', 'a', 2, 'character', + 'names_column', 'n', 2, 'integer', + 'xlab', 'x', 2, 'character', + 'log', 'g', 2, 'logical', + 'col', 'c', 2, 'list', + 'bottom_margin', 'b', 2, 'integer', + 'left_margin', 'l', 2, 'integer', + 'top_margin', 't', 2, 'integer', + 'right_margin', 'r', 2, 'integer', + 'legend_pos','e',2,'character', + 'replace_null','u',2,'logical', + 'order','w',2,'logical', + 'header','y',2,'logical' +), byrow=TRUE, ncol=4); + +options = getopt(option_specification); + +header = TRUE +if(!is.null(options$header)) header = options$header + +data = read.table(options$input_file, sep = '\t', h = header) +if(!is.null(options$replace_null) && options$replace_null){ + data[data == 0] = NA +} +if(!is.null(options$order) && options$order){ + order = order(data[,2]) + data = data[order,] +} + + +data_columns = c(2,3) +if(!is.null(options$data_columns)){ + data_columns = unlist(strsplit(options$data_columns, split=",")) + data_columns = sapply(data_columns,as.integer) + } +names_column = 1 +if(!is.null(options$names_column)) names_column = options$names_column + +margin = c(5,19,1,1) +if(!is.null(options$bottom_margin)) margin[1] = options$bottom_margin +if(!is.null(options$left_margin)) margin[2] = options$left_margin +if(!is.null(options$top_margin)) margin[3] = options$top_margin +if(!is.null(options$right_margin)) margin[4] = options$right_margin + +xlab = "" +if(!is.null(options$xlab)) xlab = options$xlab + +col = c('blue','red') +if(!is.null(options$col)) col = unlist(strsplit(options$col, split=",")) + +log = "" +if(!is.null(options$log) && options$log) log = "x" + +legend_pos="topright" +if(!is.null(options$legend_pos)) legend_pos = options$legend_pos + +names = c('Sample1','Sample2') + +if(!is.null(options$names)) names = unlist(strsplit(options$names, split=",")) +plot_barplot <- function(){ + par(las=2) + par(mar=margin) + barplot(t(data[, data_columns]), horiz = T, xlab = xlab, beside=TRUE, + names.arg = data[, names_column], col = col, cex.names=0.7, + cex.axis = 0.8, log = log) + legend(legend_pos, legend = names, fill = col, cex = 0.7) +} + +if(!is.null(options$output_pdf_file)){ + pdf(options$output_pdf_file) + plot_barplot() + dev.off() +} + +if(!is.null(options$output_svg_file)){ + svg(options$output_svg_file) + plot_barplot() + dev.off() +} \ No newline at end of file |
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| diff -r 000000000000 -r 6c9aac0d6ca2 plot_grouped_barplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_grouped_barplot.xml Mon Apr 18 10:08:25 2016 -0400 |
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| @@ -0,0 +1,145 @@ +<tool id="plot_grouped_barplot" name="Plot grouped barplot" version="0.1.0"> + <description>with R</description> + + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.20.0">r-getopt</requirement> + </requirements> + + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + + <version_command></version_command> + + <command><![CDATA[ + Rscript $__tool_directory__/plot_grouped_barplot.R + --input_file $input_file + --header $header + + #if str($output_format)=="pdf" + --output_pdf_file $output_pdf_file + #else + --output_svg_file $output_svg_file + #end if + + #set $column_with_data="" + #set $colors="" + #set $names="" + #set $sep="" + #for sample in $samples: + #set $column_with_data = $column_with_data + $sep + str($sample.column_id) + #set $colors = $colors + $sep + str($sample.color) + #set $names = $names + $sep +str($sample.name) + #set $sep="," + #end for + #set $column_with_data = $column_with_data + #set $colors = $colors + #set $names = $names + + --data_column $column_with_data + --col "$colors" + --names "$names" + --replace_null $replace_null + --order $order + --names_column $names_column + --xlab "$xlab" + --log $log + --bottom_margin $bottom_margin + --left_margin $left_margin + --top_margin $top_margin + --right_margin $right_margin + --legend_pos $legend_pos + ]]></command> + + <inputs> + <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/> + + <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/> + + <param name="output_format" label="Format for output image" type="select" help=""> + <option value="pdf" selected="True">PDF</option> + <option value="svg">SVG</option> + </param> + + <repeat name="samples" title="Add sample information (column id, name, color)" > + <param name="name" type="text" label="Name of the data" help="(--sample_name)"/> + <param name="column_id" type="data_column" data_ref="input_file" label="Column containing corresponding data" multiple="false" numerical="true" help="(after normalization, --charact_input_file)"/> + <param name="color" label="Bar color" type="text" value= "blue" help="R color (--col)"/> + </repeat> + <param name="replace_null" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Replace null values by NA?" help="(--replace_null)"/> + <param name="order" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Order given the first chosen data?" help="(--order)"/> + + <param name="names_column" type="data_column" data_ref="input_file" multiple="false" numerical="false" label="Column containing data names?" help="(--names_column)" /> + + <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/> + + <param name="log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log scale?" help="(--log)"/> + + <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/> + <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/> + <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/> + <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/> + <param name="legend_pos" label="Position of the legend" type="select" help=""> + <option value="topright" selected="True">Top right</option> + <option value="topleft">Top left</option> + <option value="bottomright">Bottom right</option> + <option value="bottomleft">Bottom left</option> + </param> + </inputs> + + <outputs> + <data name="output_pdf_file" format="pdf" + label="${tool.name} on ${on_string}: PDF barplot"> + <filter>output_format=="pdf"</filter> + </data> + <data name="output_png_file" format="png" + label="${tool.name} on ${on_string}: PNG barplot"> + <filter>output_format=="png"</filter> + </data> + <data name="output_svg_file" format="svg" + label="${tool.name} on ${on_string}: SVG barplot"> + <filter>output_format=="svg"</filter> + </data> + </outputs> + + <tests> + <test> + <param name="input_file" value="input_file.txt"/> + <param name='header' value="FALSE"/> + <param name="output_format" value="pdf"/> + <param name="samples_0|name" value="A"/> + <param name="samples_0|column_id" value="2"/> + <param name="samples_0|color" value="blue"/> + <param name="samples_1|name" value="B"/> + <param name="samples_1|column_id" value="3"/> + <param name="samples_1|color" value="red"/> + <param name="replace_null" value="FALSE"/> + <param name="order" value="FALSE"/> + <param name="names_column" value="1"/> + <param name='xlab' value=""/> + <param name='log' value="FALSE"/> + <param name='bottom_margin' value="5"/> + <param name="left_margin" value="19"/> + <param name='top_margin' value="1"/> + <param name='right_margin' value="1"/> + <param name="legend_pos" value="topright"/> + <output name="output_pdf_file" file="output_file.pdf"/> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +This tool plot a grouped barplot with multiple data: + +.. image:: $PATH_TO_IMAGES/output.png + :scale: 50 % + +This tool relies on R's barplot function. The input file must be a tabular file with multiple columns: a column with row names (for bar names) and a least a column with data. The output image is customizable (margin, legend positions, ...) and can be export in different format. + ]]></help> + + <citations> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 6c9aac0d6ca2 test-data/input_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_file.txt Mon Apr 18 10:08:25 2016 -0400 |
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| @@ -0,0 +1,18 @@ +Replication initiation protein, truncated 0.195633 0.0431745 +Resolvase, putative 0.00060098 0.183306 +UniRef50_Q8CU99 0.173071 0.0296448 +Integrase 0.303569 0.0580151 +Replication initiation protein 0.857353 0.165635 +UniRef50_Z6ILY0 0.202075 0.0208634 +UniRef50_W1W6K4 0.248059 0.0318689 +UniRef50_F0RR64 0.000754535 0.152705 +Tetracycline resistance protein 0.51126 0.101236 +Plasmid recombination enzyme 0.214064 0.0334602 +Transposase, putative 0.00200612 0.562101 +putative transposase 0.000927295 0.113753 +Plasmid recombination enzyme type 3 0.660463 0.123898 +Toxin antitoxin system, antitoxin component 0 0.142345 +Transposase IS4 family protein 0.00381025 0.4416 +hypothetical protein DR_1761 0.00032663 0.185976 +UniRef50_Q9RV33 0.000328875 0.144057 +Rep 0.365541 0.06664 |
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| diff -r 000000000000 -r 6c9aac0d6ca2 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Apr 18 10:08:25 2016 -0400 |
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| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.2.1"> + <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="r-getopt" version="1.20.0"> + <repository changeset_revision="712cb82311a8" name="package_r_3_2_1_getopt_1_20_0" owner="bebatut" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |
