comparison hetbox.xml @ 3:479f860eb8a9 draft

updated tool xml description

2:57c5ea9c3c5c

<tool id="hetbox" version="1.0" name="Minor variant boxplot">
  <description> from allele counts</description>
  <requirements>
    <requirement type="package" version="2.15.0">R</requirement>
    <requirement type="package" version="2.2.6">rpy2</requirement>
    <requirement type="package" version="1.7.1">numpy</requirement>
  </requirements>
  <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 potential contamination 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"/>

.. class:: infomark

**What it does**

Given a table with sample ids and minor alelles frequencies, generates boxplot per sample and 

.. class:: infomark

**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.


**Report**

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>
</tool>

3:479f860eb8a9

<tool id="hetbox" version="1.0" name="MAF boxplot">
  <description></description>
  <requirements>
    <requirement type="package" version="2.15.0">R</requirement>
    <requirement type="package" version="2.2.6">rpy2</requirement>
    <requirement type="package" version="1.7.1">numpy</requirement>
  </requirements>
  <command interpreter="python">hetbox.py $input $outplot $outreport
  </command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input allele counts table"/>
    <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also generate a report on data spread" />
  </inputs>
  <outputs>
    <data name="outplot" format="png" label="${tool.name} on ${on_string}: boxplot"/>
    <data name="outreport" format="tabular" label="${tool.name} on ${on_string}: report">
      <filter>report is True</filter>
    </data>
  </outputs>
  <stdio>
    <exit_code range="1:" err_level="fatal"/>

.. class:: infomark

**What it does**

The MAF Boxplot tool takes a table listing heteroplasmic sites per sample and their corresponding minor allele frequency.
It generates a boxplot of the minor allele frequencies per sample by default. 
Optionally, it can generate  a report including the total number of heteroplasmic sites and the median and the median absolute deviation (MAD) of the minor allele frequencies per sample.

-----

.. class:: warningmark

**Note**

Please, follow the format described below for the input file:

-----

.. class:: infomark

**Formats**

**Count alleles tool output format**

Columns::

    1.  sample id
    2.  chromosome
    3.  position
    4   counts for A's
    5.  counts for C's
    6.  counts for G's
    7.  counts for T's
    8.  Coverage
    9.  Number of alleles passing frequency threshold
    10. Major allele
    11. Minor allele
    12. Minor allele frequency in position

-----

**Citation**

If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.*
(boris-at-bx.psu.edu)


  </help>
</tool>