Mercurial > repos > nick > minor_variant_boxplot

annotate hetbox.xml @ 7:a777a76205cc draft default tip

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Current version - documentation and suppressing error on stderr messages
author nick
date Tue, 04 Jun 2013 00:07:06 -0400
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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 <command interpreter="python">hetbox.py $input $outplot $outreport
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4 </command>
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5 <inputs>
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6 <param name="input" type="data" format="tabular" label="Input allele counts"/>
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7 <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also produce a text report" />
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8 </inputs>
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9 <outputs>
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10 <data name="outplot" format="png"/>
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11 <data name="outreport" format="tabular">
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12 <filter>report is True</filter>
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13 </data>
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14 </outputs>
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15 <stdio>
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16 <exit_code range="1:" err_level="fatal"/>
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17 <exit_code range=":-1" err_level="fatal"/>
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18 </stdio>
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20 <help>
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21
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22 .. class:: infomark
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23
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24 **What it does**
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26 This will create a boxplot from the output of the "Count alleles" tool, showing the number of minor alleles per sample and the distribution of their frequencies (MAF). It can also, optionally, produce a text report with these numbers.
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27
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28 .. class:: infomark
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29
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30 **The boxplot**
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32 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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34 </help>
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36 <requirements>
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37 <requirement type="package" version="1.7.1">numpy</requirement>
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38 </requirements>
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39 </tool>