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1 <tool id="hetbox" version="1.0" name="Minor variant boxplot">
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2 <description> from allele counts</description>
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3 <requirements>
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4 <requirement type="package" version="2.15.0">R</requirement>
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5 <requirement type="package" version="2.2.6">rpy2</requirement>
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6 <requirement type="package" version="1.7.1">numpy</requirement>
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7 </requirements>
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8 <command interpreter="python">hetbox.py $input $outplot $outreport
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9 </command>
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10 <inputs>
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11 <param name="input" type="data" format="tabular" label="Input allele counts"/>
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12 <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also produce a potential contamination report" />
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13 </inputs>
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14 <outputs>
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15 <data name="outplot" format="png"/>
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16 <data name="outreport" format="tabular">
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17 <filter>report is True</filter>
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18 </data>
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19 </outputs>
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20 <stdio>
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21 <exit_code range="1:" err_level="fatal"/>
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22 <exit_code range=":-1" err_level="fatal"/>
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23 </stdio>
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24
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25 <help>
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26
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27 .. class:: infomark
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28
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29 **What it does**
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30
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31 Given a table with sample ids and minor alelles frequencies, generates boxplot per sample and
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32
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33 .. class:: infomark
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34
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35 **Boxplot**
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36
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37 The graphic shows the distribution of the minor allele frequencies as a boxplot per sample. At the bottom of each plot, a count (N) is given of the number of minor alleles in the plot.
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38
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39
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40 **Report**
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41
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42 The graphic shows the distribution of the minor allele frequencies as a boxplot per sample. At the bottom of each plot, a count (N) is given of the number of minor alleles in the plot.
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43
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44
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45
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46 </help>
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47 </tool> |
