Mercurial > repos > iuc > gemini_de_novo

annotate gemini_de_novo.xml @ 0:285f519dab87 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:57:08 -0500
parents
children 4aabe53ecfe0
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285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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2 <description>Identifying potential de novo mutations</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">de_novo</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 gemini @BINARY@
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14 #if $report.report_selector != 'all':
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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15 --columns "${report.columns}"
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16 #end if
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18 @CMDLN_SQL_FILTER_FILTER_OPTION@
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20 #if int($min_kindreds) > 0:
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21 --min-kindreds $min_kindreds
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22 #end if
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24 #if str($families).strip():
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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25 --families "$families"
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26 #end if
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27
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28 $lenient
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29 $allow_unaffected
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30
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285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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32 -d $d
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33
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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34 #if int($min_gq) > 0:
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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35 --min-gq $min_gq
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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36 #end if
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285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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38 #if int($gt_pl_max) > -1:
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39 --gt-pl-max $gt_pl_max
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40 #end if
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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43 "${ infile }"
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44 > "${ outfile }"
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45 ]]>
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46 </command>
285f519dab87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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47 <inputs>
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48 <expand macro="infile" />
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49 <expand macro="column_filter" />
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50 <expand macro="filter" />
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51 <expand macro="min_kindreds" />
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52 <expand macro="family" />
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53 <expand macro="lenient" />
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54 <expand macro="unaffected" />
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55 <expand macro="min_sequence_depth" />
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56 <expand macro="min_gq" />
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57 <expand macro="gt_pl_max" />
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58 </inputs>
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59 <outputs>
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60 <data name="outfile" format="tabular" />
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
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65 <param name="columns" value="gene,ref,alt,impact" />
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66 <output name="outfile" file="gemini_de_novo_result.tabular" />
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67 </test>
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68 </tests>
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69 <help>
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70 **What it does**
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71
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72 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
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73 you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring.
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74
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75 </help>
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76 <expand macro="citations"/>
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77 </tool>