| Previous changeset 1:d3d92fb20389 (2017-08-29) Next changeset 3:63a595b451d1 (2019-02-11) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf |
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modified:
ggplot_histogram.xml macros.xml test-data/mtcars.txt |
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added:
test-data/ggplot_heatmap_result1.pdf test-data/ggplot_pca_result1.pdf |
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| diff -r d3d92fb20389 -r f52035800250 ggplot_histogram.xml --- a/ggplot_histogram.xml Tue Aug 29 09:02:13 2017 -0400 +++ b/ggplot_histogram.xml Mon Jun 11 16:05:18 2018 -0400 |
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| @@ -1,9 +1,10 @@ -<tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@"> +<tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@+galaxy0"> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="1.4.2">r-reshape2</requirement> + <requirement type="package" version="1.4.3">r-reshape2</requirement> + <requirement type="package" version="1.2.1">r-svglite</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ cat '$script' && @@ -11,61 +12,59 @@ ]]></command> <configfiles> <configfile name="script"><![CDATA[ - @R_INIT@ ## Import library -library("reshape2") -library("ggplot2") +library(reshape2) +library(ggplot2) integrated <- read.csv('$input1', sep='\t', header=TRUE) input <- melt(integrated) -## Show/hide legend -#if $legend == "yes" - gg_legend = NULL -#else - gg_legend = theme(legend.position="none") -#end if +@LEGEND@ ## density -#if $density == "counts" +#if $adv.density == "counts" gg_density = ggplot(input,aes(value, color=variable)) gg_freq = NULL -#elif $density == "nfreq" +#elif $adv.density == "nfreq" gg_density = ggplot(input,aes(value, ..ncount.., color=variable)) gg_freq = NULL -#elif $density == "freq" +#elif $adv.density == "freq" gg_density = ggplot(input,aes(value, color=variable)) gg_freq = aes(y=..count../sum(..count..)) #end if +@TRANSFORM@ + @XY_SCALING@ -gg_width = $with_output_dim -gg_height = $height_output_dim - +@THEME@ -@TRANSFORM@ - -#if $facet == "facet" +#if $adv.facet == "facet" gg_facet = facet_wrap(~ variable) #else gg_facet = NULL #end if -#if $coloring.colorscheme == "Default" +#if $adv.coloring.colorscheme == "Default" gg_colorscale = NULL #else - gg_colorscale = scale_color_brewer(palette=$coloring.colors, direction=$coloring.colororder) + gg_colorscale = scale_color_brewer(palette=$adv.coloring.colors, direction=$adv.coloring.colororder) #end if -gg_density+ -geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size)+gg_facet+gg_colorscale+ -gg_scalex+gg_scaley+theme_bw()+xlab('$xlab')+ylab('$ylab')+gg_legend+ggtitle('$title') +plot_out <- gg_density + + geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size) + gg_facet + gg_colorscale + + gg_scalex + + gg_scaley + + gg_theme + + xlab('$xlab') + + ylab('$ylab') + + gg_legend + + ggtitle('$title') + + theme(plot.title = element_text(hjust = 0.5)) -ggsave(file='Rplot.pdf') -dev.off() +@SAVE_OUTPUT@ ]]></configfile> </configfiles> <inputs> @@ -74,54 +73,51 @@ <expand macro="xy_lab" /> <param name="size" type="float" value="1.0" label="relative line width" /> <param name="binwidth" type="float" value="0.5" label="Bin width for plotting"/> - - <expand macro="transform" /> - - <param name="density" type="select" label="Advanced - plot counts or density"> - <option value="counts">Plot counts on the y-axis</option> - <option value="freq">Plot frequency on the y-axis</option> - <option value="nfreq">Plot normalized frequency on the y-axis</option> - </param> - <param name="facet" type="select" label="Advanced - faceting"> - <option value="none">Plot my groups on one plot</option> - <option value="facet">Plot my groups on individual plots</option> - </param> - <conditional name="coloring"> - <param name="colorscheme" type="select" label="Advanced - coloring groups" > - <option value="Default" selected="True">No thanks - just use the default scheme to color code my groups (columns)</option> - <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="density" type="select" label="Plot counts or density"> + <option value="counts">Plot counts on the y-axis</option> + <option value="freq">Plot frequency on the y-axis</option> + <option value="nfreq">Plot normalized frequency on the y-axis</option> + </param> + <param name="facet" type="select" label="Faceting"> + <option value="none">Plot my groups on one plot</option> + <option value="facet">Plot my groups on individual plots</option> </param> - <when value="Default"> - </when> - <when value="Defined"> - <expand macro="colors" /> - <param name="colororder" type="select" label="Reverse color scheme" > - <option value="1">Default order of color scheme</option> - <option value="-1">Reverse the order of my color scheme</option> - </param> - </when> - </conditional> - <expand macro="xy_scaling" /> - <expand macro="dimensions" /> - <param name="legend" type="select" label="Legend options"> - <option value="yes">Include legend on plot</option> - <option value="no">Hide legend</option> - </param> + <conditional name="coloring"> + <param name="colorscheme" type="select" label="Coloring groups" > + <option value="Default" selected="true">No thanks - just use the default scheme to color code my groups (columns)</option> + <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option> + </param> + <when value="Default"> + </when> + <when value="Defined"> + <expand macro="colors" /> + <param name="colororder" type="select" label="Reverse color scheme" > + <option value="1">Default order of color scheme</option> + <option value="-1">Reverse the order of my color scheme</option> + </param> + </when> + </conditional> + <expand macro="transform" /> + <expand macro="xy_scaling" /> + <expand macro="theme" /> + <expand macro="legend" /> + </section> + <section name="out" title="Output Options" expanded="true"> + <expand macro="dimensions" /> + </section> </inputs> <outputs> - <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> - ToDo: It would be nice to have different output formats for all tools - --> - <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/> + <expand macro="additional_output" /> </outputs> <tests> <test> <param name="input1" value="mtcars.txt"/> - <output name="output1" file="ggplot_histogram_result1.pdf" compare="sim_size"/> + <param name="additional_output_format" value="pdf" /> + <output name="output2" file="ggplot_histogram_result1.pdf" compare="sim_size"/> </test> </tests> <help><![CDATA[ - This tool will generate a histogram representing the distrinutions of each numerical column. Each column should have a descriptive header with no spaces, which will be used in the plot legend to represent the corresponding column (group). Input data example: @@ -132,7 +128,6 @@ gene_D 6 9 gene_E 9 13.5 gene_F 8 12 - ]]></help> <expand macro="citations"/> </tool> |
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| diff -r d3d92fb20389 -r f52035800250 macros.xml --- a/macros.xml Tue Aug 29 09:02:13 2017 -0400 +++ b/macros.xml Mon Jun 11 16:05:18 2018 -0400 |
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| b'@@ -9,27 +9,116 @@\n <token name="@VERSION@">2.2.1</token>\n \n <token name="@R_INIT@"><![CDATA[\n-## Setup R error handling to go to stderr\n-options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})\n+ ## Setup R error handling to go to stderr\n+ options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})\n \n-## Unify locale settings\n-loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n+ ## Unify locale settings\n+ loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")\n ]]></token>\n \n <token name="@TRANSFORM@"><![CDATA[\n-#if $transform == "log2"\n- input["value"] <- log2(input["value"])\n-#elif $transform == "log2plus1"\n- input["value"] <- log2(input["value"]+1)\n-#elif $transform == "log10"\n- input["value"] <- log10(input["value"])\n-#elif $transform == "log10plus1"\n- input["value"] <- log10(input["value"]+1)\n-#end if\n+ #if $adv.transform == "log2"\n+ input["value"] <- log2(input["value"])\n+ #elif $adv.transform == "log2plus1"\n+ input["value"] <- log2(input["value"]+1)\n+ #elif $adv.transform == "log10"\n+ input["value"] <- log10(input["value"])\n+ #elif $adv.transform == "log10plus1"\n+ input["value"] <- log10(input["value"]+1)\n+ #end if\n+ ]]></token>\n+\n+ <token name="@XY_SCALING@"><![CDATA[\n+ #Choose between automatically scaled x and y axis or user defined\n+ #if $adv.scaling.plot_scaling == "Automatic"\n+ gg_scalex = NULL\n+ gg_scaley = NULL\n+ #else\n+ gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)\n+ gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)\n+ cat("\\n xaxismin: ", $adv.scaling.xaxismin)\n+ cat("\\n xaxismax: ", $adv.scaling.xaxismax)\n+ cat("\\n yaxismin: ", $adv.scaling.yaxismin)\n+ cat("\\n yaxismax: ", $adv.scaling.yaxismax)\n+ #end if\n+ ]]></token>\n+\n+ <token name="@THEME@"><![CDATA[\n+ ## Choose theme for plot\n+ #if $adv.theme == "bw"\n+ gg_theme = theme_bw()\n+ #else\n+ gg_theme = NULL\n+ #end if\n ]]></token>\n \n+ <token name="@LEGEND@"><![CDATA[\n+ ## Show/hide legend\n+ #if $adv.legend == "yes"\n+ gg_legend = theme(legend.position="right")\n+ #else\n+ gg_legend = theme(legend.position="none")\n+ cat("\\n no legend")\n+ #end if\n+ ]]></token>\n+ <token name="@SAVE_OUTPUT@"><![CDATA[\n+ ## output options need to be in out section\n+ gg_width <- as.double(\'$out.width_output_dim\')\n+ gg_height <- as.double(\'$out.height_output_dim\')\n+ gg_unit <- \'$out.unit_output_dim\'\n+ gg_dpi <- as.double(\'$out.dpi_output_dim\')\n+ gg_add_device <- \'$out.additional_output_format\'\n+ output1 <- \'$output1\'\n+ output2 <- \'$output2\'\n+\n+ ## ggsave to png\n+ ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")\n+ if(gg_add_device != "none"){\n+ ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)\n+ }\n+ ]]></token>\n+ <xml name="read_complex_input">\n+ <param name="input1" type="data" format="tabular" label="Select table"/>\n+ <conditional name="inputdata">\n+ <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">\n+ <option value="with_header" selected="true">Dataset with header</option>\n+ <option value="with_rownames">Dataset with row names</option>\n+ <option value="with_header_rownames">Dataset with header and row names</option>\n+ <option value="no_header_rownames">Dataset without header or row names</opt'..b'="dpi of output" help="Plot resolution. Applies only to raster output types."/>\n+ <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format">\n+ <option value="none" selected="true">only PNG</option>\n+ <option value="pdf">PDF</option>\n+ <option value="svg">SVG</option>\n+ <option value="eps">EPS</option>\n+ <option value="ps">PS</option>\n+ <option value="tex">TEX (pictex)</option>\n+ <option value="jpeg">JPEG</option>\n+ <option value="tiff">TIFF</option>\n+ <option value="bmp">BMP</option>\n+ </param>\n </xml>\n <xml name="citations">\n <citations>\n- <citation type="bibtex">@Book{\n+ <citation type="bibtex">@book{wickham2009ggplot2,\n author = {Hadley Wickham},\n title = {ggplot2: Elegant Graphics for Data Analysis},\n publisher = {Springer-Verlag New York},\n year = {2009},\n isbn = {978-0-387-98140-6},\n- url = {http://ggplot2.org}\n+ url = {http://ggplot2.org},\n }\n </citation>\n+ <yield />\n </citations>\n </xml>\n-\n- <xml name="axis_customization" token_label="Advanced - axis title options">\n+ <xml name="axis_customization" token_label="Axis title options">\n <param name="axis_customization" type="select" label="@LABEL@">\n- <option value="default" selected="True">Default</option>\n+ <option value="default" selected="true">Default</option>\n <option value="defined">User defined label options</option>\n </param>\n <when value="default">\n@@ -113,7 +225,7 @@\n <option value="magenta">Magenta</option>\n <option value="cyan">Cyan</option>\n <option value="grey">Grey</option>\n- <option value="gold">Gold</option> \n+ <option value="gold">Gold</option>\n </param>\n <param name="face" type="select" label="Font effect of axis label">\n <option value="plain">Normal (default)</option>\n@@ -122,7 +234,6 @@\n </param>\n </when>\n </xml>\n-\n <xml name="colors">\n <param name="colors" type="select" label="Color schemes to differentiate your groups" >\n <option value="Default">Default color scheme</option>\n@@ -159,8 +270,22 @@\n <option value="RdBu">Red to blue (discrete, max=11 colors)</option>\n <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>\n <option value="PRGn">Purple to green (discrete, max=11 colors)</option>\n- <option value="BrBG">Brown to teal (discrete, max=11 colors)</option> \n+ <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>\n </param>\n </xml>\n-\n+ <xml name="additional_output">\n+ <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>\n+ <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">\n+ <change_format>\n+ <when input="out.additional_output_format" value="svg" format="svg" />\n+ <when input="out.additional_output_format" value="eps" format="eps" />\n+ <when input="out.additional_output_format" value="ps" format="ps" />\n+ <when input="out.additional_output_format" value="tex" format="txt" />\n+ <when input="out.additional_output_format" value="jpeg" format="jpg" />\n+ <when input="out.additional_output_format" value="tiff" format="tiff" />\n+ <when input="out.additional_output_format" value="bmp" format="bmp" />\n+ </change_format>\n+ <filter>out[\'additional_output_format\'] != "none"</filter>\n+ </data>\n+ </xml>\n </macros>\n' |
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