Mercurial > repos > boris > hetbox
diff hetbox.xml @ 0:8d2c4c11fd8f draft default tip
Uploaded repo.tar.gz
author | boris |
---|---|
date | Mon, 03 Feb 2014 13:15:10 -0500 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hetbox.xml Mon Feb 03 13:15:10 2014 -0500 @@ -0,0 +1,75 @@ +<tool id="hetbox" version="1.0" name="MAF boxplot"> + <description>Minor Allele Frequency Boxplot</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"/> + <exit_code range=":-1" err_level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**What it does** + +The MAF Boxplot tool takes a table listing heteroplasmic sites per sample and their corresponding minor allele frequency (MAF). +It generates a boxplot of the minor allele frequencies per sample by default. The number of heteroplasmic sites is displayed under each box. +Optionally, it can generate a report that includes the total number of heteroplasmic sites, 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** + +**Variant Annotator 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> \ No newline at end of file