Mercurial > repos > boris > hetbox
changeset 3:479f860eb8a9 draft
updated tool xml description
| author | boris |
|---|---|
| date | Tue, 25 Jun 2013 00:50:46 -0400 |
| parents | 57c5ea9c3c5c |
| children | 1c21e9f3104b |
| files | hetbox.xml |
| diffstat | 1 files changed, 39 insertions(+), 11 deletions(-) [+] |
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--- a/hetbox.xml Fri Jun 21 16:05:46 2013 -0400 +++ b/hetbox.xml Tue Jun 25 00:50:46 2013 -0400 @@ -1,5 +1,5 @@ -<tool id="hetbox" version="1.0" name="Minor variant boxplot"> - <description> from allele counts</description> +<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> @@ -8,12 +8,12 @@ <command interpreter="python">hetbox.py $input $outplot $outreport </command> <inputs> - <param name="input" type="data" format="tabular" label="Input allele counts"/> - <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also produce a potential contamination report" /> + <param name="input" type="data" format="tabular" label="Input allele counts table"/> + <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also generate a report on data spread" /> </inputs> <outputs> - <data name="outplot" format="png"/> - <data name="outreport" format="tabular"> + <data name="outplot" format="png" label="${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> @@ -28,19 +28,47 @@ **What it does** -Given a table with sample ids and minor alelles frequencies, generates boxplot per sample and +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 -**Boxplot** +**Formats** -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. +**Count alleles tool output format** +Columns:: -**Report** + 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 -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. +----- +**Citation** + +If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.* +(boris-at-bx.psu.edu) </help>