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