Mercurial > repos > moheydarian > heatmap2
changeset 4:d61d62699e5c draft
Uploaded
| author | moheydarian |
|---|---|
| date | Tue, 14 Mar 2017 14:20:49 -0400 |
| parents | f4e9535003ad |
| children | d0a63c827053 |
| files | ggplot_histogram.xml |
| diffstat | 1 files changed, 185 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ggplot_histogram.xml Tue Mar 14 14:20:49 2017 -0400 @@ -0,0 +1,185 @@ +<tool id="ggplot_histogram" name="Histogram w ggplot2" version="0.1.2"> + <requirements> + <requirement type="package">r-getopt</requirement> + <requirement type="package">r-ggplot2</requirement> + <requirement type="package">r-reshape2</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + Rscript ${__tool_directory__}/ggplotscripthistogram.R --input "$input1" --title "$title" + --xlab "$xlab" --ylab "$ylab" --transform "$transformation.transform" --scaling "$scaling.Plot_scaling" + --colorscheme "$coloring.colorscheme" --dim "$dimensions.plotdim" --facet "$group.facet" + --size "$size" --binwidth "$binwidth" --legend "$showlegend.legend" --output "Rplot.pdf" + #if str( $coloring.colorscheme ) == "Defined": + --colors ${coloring.colors} + --colororder ${coloring.colororder} + #else: + --colors=irrelevant + --colororder=1 + #end if + + #if str( $scaling.Plot_scaling ) == "Defined": + --xaxismin=${scaling.xaxismin} + --xaxismax=${scaling.xaxismax} + --yaxismin=${scaling.yaxismin} + --yaxismax=${scaling.yaxismax} + #else: + --xaxismin=0 + --xaxismax=1 + --yaxismin=2 + --yaxismax=3 + #end if + + #if str( $dimensions.plotdim ) == "Defined": + --woutputdim ${dimensions.woutputdim} + --houtputdim ${dimensions.houtputdim} + #else: + --woutputdim=7 + --houtputdim=7 + #end if + + ]]></command> + <inputs> + <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/> + <param name="title" size="30" type="text" format="txt"/> + <param name="xlab" size="30" type="text" value="title of x-axis" label="Label for x-axis"/> + <param name="ylab" size="30" type="text" value="title of y-axis" label="Label for y-axis"/> + <param name="size" size="4" type="float" value="1" label="relative line width" /> + <param name="binwidth" size="4" type="float" value="0.5" label="Bin width for plotting"/> + <conditional name="transformation"> + <param name="transform" type="select" label="Advanced - log transformation"> + <option value="none">Plot the data as it is</option> + <option value="log2">Log2(value) transform my data</option> + <option value="log2plus1">Log2(value+1) transform my data</option> + <option value="log10">Log10(value) transform my data</option> + <option value="log10plus1">Log10(value+1) transform my data</option> + </param> + </conditional> + <conditional name="group"> + <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> + <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> + </param> + <when value="Default"> + </when> + <when value="Defined"> + <param name="colors" type="select" label="Color schemes to differentiate your groups" > + <option value="Default">Default color scheme</option> + <option value="YlOrRd">Yellow to orange to red (discrete, max=9 colors)</option> + <option value="YlOrBr">Yellow to orange to brown (discrete, max=9 colors)</option> + <option value="YlGnBu">Yellow to green to blue (discrete, max=9 colors)</option> + <option value="YlGn">Yellow to green (discrete, max=9 colors)</option> + <option value="Reds">Shades of red from light to dark (discrete, max=9 colors)</option> + <option value="RdPu">Red to purple (discrete, max=9 colors)</option> + <option value="Purples">Shades of purple from light to dark (discrete, max=9 colors)</option> + <option value="PuRd">Purple to red (discrete, max=9 colors)</option> + <option value="PuBuGn">Purple to blue to green (discrete, max=9 colors)</option> + <option value="PuBu">Purple to blue(discrete, max=9 colors)</option> + <option value="OrRd">Orange to red (discrete, max=9 colors)</option> + <option value="Oranges">Shades of orange from light to dark (discrete, max=9 colors)</option> + <option value="Greys">Shades of grey from light to dark (discrete, max=9 colors)</option> + <option value="Greens">Shades of greens from light to dark (discrete, max=9 colors)</option> + <option value="GnBu">Green to blue (discrete, max=9 colors)</option> + <option value="BuPu">Blue to purple (discrete, max=9 colors)</option> + <option value="BuGn">Blue to green (discrete, max=9 colors)</option> + <option value="Blues">Shades of blue from light to dark (discrete, max=9 colors)</option> + <option value="Set1">Set 1 - predefined color pallete (discrete, max=9 colors)</option> + <option value="Set2">Set 2 - predefined color pallete (discrete, max=8 colors)</option> + <option value="Set3">Set 3 - predefined color pallete (discrete, max=12 colors)</option> + <option value="Pastel1">Pastel 1 - predefined pastel color pallete (discrete, max=9 colors)</option> + <option value="Pastel2">Pastel 2 - predefined pastel color pallete (discrete, max=8 colors)</option> + <option value="Paired">Paired - predefined color pallete (discrete, max=12 colors)</option> + <option value="Dark2">Dark 2 - predefined color pallete (discrete, max=12 colors)</option> + <option value="Accent">Accent - predefined color pallete (discrete, max=12 colors)</option> + <option value="Spectral">Spectral - Red to yellow to purple (discrete, max=11 colors)</option> + <option value="RdYlGn">Red to yellow to green (discrete, max=11 colors)</option> + <option value="RdYlBu">Red to yellow to blue (discrete, max=11 colors)</option> + <option value="RdGy">Red to grey (discrete, max=11 colors)</option> + <option value="RdBu">Red to blue (discrete, max=11 colors)</option> + <option value="PuOr">Purple to orange (discrete, max=11 colors)</option> + <option value="PRGn">Purple to green (discrete, max=11 colors)</option> + <option value="BrBG">Brown to teal (discrete, max=11 colors)</option> + </param> + <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> + <conditional name="scaling"> + <param name="Plot_scaling" type="select" label="Advanced - Axis scaling"> + <option value="Automatic" selected="True">Automatic axis scaling</option> + <option value="Defined">User deined axis scales</option> + </param> + <when value="Automatic"> + <!--Do nothing here --> + </when> + <when value="Defined"> + <param name="xaxismin" size="4" type="integer" value="0" label="minimal range of x-axis" /> + <param name="xaxismax" size="4" type="integer" value="3" label="maximal range of x-axis" /> + <param name="yaxismin" size="4" type="integer" value="0" label="minimal range of y-axis" /> + <param name="yaxismax" size="4" type="integer" value="3" label="maximal range of y-axis" /> + </when> + </conditional> + <conditional name="dimensions"> + <param name="plotdim" type="select" label="Advanced - output dimensions"> + <option value="Default" selected="True">Default</option> + <option value="Defined">User deined output dimensions</option> + </param> + <when value="Default"> + <!--Do nothing here --> + </when> + <when value="Defined"> + <param name="woutputdim" size="4" type="float" value="7" label="width of output (inches)" /> + <param name="houtputdim" size="4" type="float" value="7" label="height of output (inches)" /> + </when> + </conditional> + <conditional name="showlegend"> + <param name="legend" type="select" label="Legend options"> + <option value="yes">Include legend on plot</option> + <option value="no">Hide legend</option> + </param> + </conditional> + </inputs> + <outputs> + <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> --> + <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/> + </outputs> + <tests> + <test> + <param name="input1" value="input.txt"/> + <output name="output1" file="Rplot.pdf"/> + </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: +ID Cond_A Cond_B +gene_A 10 15 +gene_B 8 12 +gene_C 10 15 +gene_D 6 9 +gene_E 9 13.5 +gene_F 8 12 + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{renameTODO, + author = {TODO, FirstTODO}, + year = {TODO}, + title = {TODO}, + url = {under construction}, +}</citation> + </citations> +</tool>