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1 <tool id="roary_plots" name="Roary plots" version="1.0">
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2 <description>Generate plots from Roary outputs</description>
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1
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3 <requirements>
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4 <requirement type="package" version="1.78">biopython</requirement>
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5 <requirement type="package" version="3.4.2">matplotlib</requirement>
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6 <requirement type="package" version="1.20.2">numpy</requirement>
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7 <requirement type="package" version="1.2.4">pandas</requirement>
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8 <requirement type="package" version="0.11.1">seaborn</requirement>
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9 </requirements>
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10
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3
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11 <command>${__tool_directory__}/Roary/contrib/roary_plots/roary_plots.py --labels $tree $input ;cp pangenome_matrix.png $heatmap; cp -rf pangenome_frequency.png $frequency; cp -rf pangenome_pie.png $pie</command>
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12
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13
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14 <inputs>
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15 <param format="csv" name="input" type="data" label="Gene Presence Absence matrix"/>
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16 <param format="newick" name="tree" type="data" label="Newick"/>
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17
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18 </inputs>
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19
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20 <outputs>
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21 <data format="png" name="heatmap" label="Pangenome matrix tree"/>
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22 <data format="png" name="frequency" label="Pangenome frequency"/>
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23 <data format="png" name="pie" label="Pangenome pie"/>
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24 </outputs>
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25
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26 <help>
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27 For full documentation, please go to the Roary plots website : https://github.com/sanger-pathogens/Roary/tree/master/contrib/roary_plots
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28
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29 </help>
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30
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31 </tool>
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