Mercurial > repos > immport-devteam > flowtext_scatterplot
view getDensityPlots_text.xml @ 1:754d511df1a3 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowtext_scatterplot commit 2944aa6b74efcdb8d5cbf31abf27b352dcad9ac9"
author | azomics |
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date | Tue, 14 Jul 2020 09:40:13 -0400 |
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<tool id="gen_density_plots_txt" name="Generate scatter plots" version="1.1+galaxy0" profile="18.01"> <description>for any given markers in a txt-converted FCS file</description> <requirements> <requirement type="package" version="3.3.2">r-ggplot2</requirement> <requirement type="package" version="2.23_17">r-kernsmooth</requirement> </requirements> <stdio> <exit_code range="1:9" level="fatal" /> <exit_code range="10" level="fatal" description="Please provide a comma separated list of channels to plot" /> <exit_code range="11" level="fatal" description="Please provide numeric values for the list of channels to plot" /> <exit_code range="12" level="fatal" description="Please provide more than one channel to plot" /> <exit_code range="13:" level="fatal"/> </stdio> <command><![CDATA[ Rscript $__tool_directory__/getDensityPlots_text.R '${input}' '${channels}' '${output}' '${outformat}' ]]> </command> <inputs> <param format="flowtext" name="input" type="data" label="txt-converted FCS file"/> <param name="channels" type="text" label="Markers to plot:" value="i.e.:1,3,4" help="By default, will plot FSC vs SSC if the channels are found."/> <param name="outformat" type="select" label="Output Format" help="PDF will be larger files that may take some time to load."> <option value="PNG">PNG</option> <option value="PDF">PDF</option> </param> </inputs> <outputs> <data format="png" name="output" label="Scatter Plots of ${channels} from ${input.name} in ${outformat}"> <change_format> <when input="outformat" value="PDF" format="pdf" /> </change_format> </data> </outputs> <tests> <test> <param name="input" value="input.flowtext"/> <param name="channels" value="i.e.:1,3,4"/> <param name="outformat" value="PDF"/> <output name="output" file="graph.pdf" compare="sim_size" delta="2000000"/> </test> <test> <param name="input" value="input.flowtext"/> <param name="channels" value="1,3,5"/> <param name="outformat" value="PNG"/> <output name="output" file="graph2.png" compare="sim_size" delta="1000000"/> </test> </tests> <help><![CDATA[ This tool allows generation of density scatter plots using ggplot2. ----- **Input files** This tool takes txt-converted FCS files as input. **Output files** This tool generates a scatter plot for each marker combination in a single png file. A pdf file can optionally be generated. class:: warningmark PDF are larger files that may take some time to load. It might be faster to download the PDF output once generated to open it locally. ----- **Example** *Output*: .. image:: ./static/images/flowtools/flowtextgraph.png ]]> </help> <citations> <citation type="bibtex">@BOOK{, author = {Hadley Wickham}, title = {ggplot2: Elegant Graphics for Data Analysis}, publisher = {Springer-Verlag New York}, year = {2009}, isbn = {978-0-387-98140-6}, url = {http://ggplot2.org}, }</citation> </citations> </tool>