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1 <tool id="BubblePlot" name="Bubbleplot" version="1">
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2 <description> </description>
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3 <requirements>
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4 <requirement type="package" >perl</requirement>
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5 <requirement type="package" >r-base</requirement>
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6 </requirements>
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7 <command> <![CDATA[
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8 ln -s $__tool_directory__/bubbleplot.R 2>$log &&
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9 ln -s $__tool_directory__/MatData.csv 2>>$log &&
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10 ln -s $__tool_directory__/VirData.csv 2>>$log &&
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11 perl $__tool_directory__/plotMdata.pl $outfile_tabular $plot1 $plot2 ${" ".join(map(str, $input_file))} 2>>$log
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="input_file" format="txt" type="data" multiple="true" label="show-snps tabular ouput" help="Clustering of SARS-CoV-2 isolates based on high-freq alleles" />
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="outfile_tabular" label="AF prevalence in SARS-CoV-2 types, as defined in Chiara et tabular format " />
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19 <data format="pdf" name="plot1" label="Bubbleplot " />
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20 <data format="pdf" name="plot2" label="Heatmap " />
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21 <data format="txt" name="log" label="${tool.name} on ${on_string}: log file "/>
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22 </outputs>
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23 <help>
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24 </help>
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25 <citations>
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26 </citations>
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27 </tool>
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