view hetbox.xml @ 7:a777a76205cc draft default tip

Current version - documentation and suppressing error on stderr messages

<tool id="hetbox" version="1.0" name="Minor variant boxplot">
  <description> from allele counts</description>
  <command interpreter="python">hetbox.py $input $outplot $outreport
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input allele counts"/>
    <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also produce a text report" />
  </inputs>
  <outputs>
    <data name="outplot" format="png"/>
    <data name="outreport" format="tabular">
      <filter>report is True</filter>
    </data>
  </outputs>
  <stdio>
    <exit_code range="1:" err_level="fatal"/>
    <exit_code range=":-1" err_level="fatal"/>
  </stdio>

  <help>

.. class:: infomark

**What it does**

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.

.. class:: infomark

**The boxplot**

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.

  </help>

  <requirements>
    <requirement type="package" version="1.7.1">numpy</requirement>
  </requirements>
</tool>