Mercurial > repos > boris > hetbox
comparison hetbox.xml @ 0:8d2c4c11fd8f draft default tip
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| author | boris |
|---|---|
| date | Mon, 03 Feb 2014 13:15:10 -0500 |
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| -1:000000000000 | 0:8d2c4c11fd8f |
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| 1 <tool id="hetbox" version="1.0" name="MAF boxplot"> | |
| 2 <description>Minor Allele Frequency Boxplot</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.15.0">R</requirement> | |
| 5 <requirement type="package" version="2.2.6">rpy2</requirement> | |
| 6 <requirement type="package" version="1.7.1">numpy</requirement> | |
| 7 </requirements> | |
| 8 <command interpreter="python">hetbox.py $input $outplot $outreport | |
| 9 </command> | |
| 10 <inputs> | |
| 11 <param name="input" type="data" format="tabular" label="Input allele counts table"/> | |
| 12 <param name="report" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Also generate a report on data spread" /> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data name="outplot" format="png" label="${tool.name} on ${on_string}: boxplot"/> | |
| 16 <data name="outreport" format="tabular" label="${tool.name} on ${on_string}: report"> | |
| 17 <filter>report is True</filter> | |
| 18 </data> | |
| 19 </outputs> | |
| 20 <stdio> | |
| 21 <exit_code range="1:" err_level="fatal"/> | |
| 22 <exit_code range=":-1" err_level="fatal"/> | |
| 23 </stdio> | |
| 24 | |
| 25 <help> | |
| 26 | |
| 27 .. class:: infomark | |
| 28 | |
| 29 **What it does** | |
| 30 | |
| 31 The MAF Boxplot tool takes a table listing heteroplasmic sites per sample and their corresponding minor allele frequency (MAF). | |
| 32 It generates a boxplot of the minor allele frequencies per sample by default. The number of heteroplasmic sites is displayed under each box. | |
| 33 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. | |
| 34 | |
| 35 ----- | |
| 36 | |
| 37 .. class:: warningmark | |
| 38 | |
| 39 **Note** | |
| 40 | |
| 41 Please, follow the format described below for the input file: | |
| 42 | |
| 43 ----- | |
| 44 | |
| 45 .. class:: infomark | |
| 46 | |
| 47 **Formats** | |
| 48 | |
| 49 **Variant Annotator tool output format** | |
| 50 | |
| 51 Columns:: | |
| 52 | |
| 53 1. sample id | |
| 54 2. chromosome | |
| 55 3. position | |
| 56 4 counts for A's | |
| 57 5. counts for C's | |
| 58 6. counts for G's | |
| 59 7. counts for T's | |
| 60 8. Coverage | |
| 61 9. Number of alleles passing frequency threshold | |
| 62 10. Major allele | |
| 63 11. Minor allele | |
| 64 12. Minor allele frequency in position | |
| 65 | |
| 66 ----- | |
| 67 | |
| 68 **Citation** | |
| 69 | |
| 70 If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.* | |
| 71 (boris-at-bx.psu.edu) | |
| 72 | |
| 73 | |
| 74 </help> | |
| 75 </tool> |