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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2 <description>perform sample-wise gene-level burden calculations</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>gemini_macros.xml</import>
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7 <token name="@BINARY@">burden</token>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 gemini @BINARY@
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12 --cases $cases
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13 --controls $controls
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14 $save_tscores
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15 $nonsynonymous
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16 $calpha
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17 --permutations $permutations
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18 #if float( str($min_aaf) ) >= 0.0:
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19 --min-aaf $min_aaf
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20 #end if
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21 #if float( str($max_aaf) ) >= 0.0:
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22 --max-aaf $max_aaf
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23 #end if
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24 "${ infile }"
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25 > "${ outfile }"
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26 ]]>
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27
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28 </command>
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29 <expand macro="stdio" />
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30 <inputs>
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2
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31 <expand macro="infile" />
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0
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32
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33 <param name="cases" size="30" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
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34 <param name="controls" size="30" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>
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35
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36 <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False"
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37 label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>
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38
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39 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False"
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40 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
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41 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False"
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42 label="Run the C-alpha association test" help="(--calpha)"/>
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43 <param name="min_aaf" type="float" value="-1" size="5" label="The min. alt. allele frequency for a variant to be included"
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44 help="(--min-aaf)">
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45 <!--validator type="in_range" min="0.0"/-->
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46 </param>
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47 <param name="max_aaf" type="float" value="-1" size="5" label="The max. alt. allele frequency for a variant to be included"
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48 help="(--max-aaf)">
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49 <!--validator type="in_range" min="0.0"/-->
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50 </param>
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51
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52 <param name="permutations" type="integer" value="1000" size="10" label="Number of permutations to run for the C-alpha test"
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53 help="(--permutations)">
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54 <validator type="in_range" min="0"/>
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55 </param>
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56
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57 </inputs>
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58 <outputs>
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2
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59 <data name="outfile" format="tabular" />
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0
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60 </outputs>
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61 <tests>
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62 <test>
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63 </test>
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64 </tests>
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65 <help>
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66 **What it does**
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67
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68 The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis.
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69 By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample.
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70
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71 $ gemini burden test.burden.db
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72 gene M10475 M10478 M10500 M128215
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73 WDR37 2 2 2 2
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74 CTBP2 0 0 0 1
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75 DHODH 1 0 0 0
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76
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77 @CITATION@
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78 </help>
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79 <expand macro="citations">
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80 <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation -->
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81 </expand>
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82 </tool>
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