Mercurial > repos > iuc > gemini_de_novo

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:59:25 -0500
parents 4aabe53ecfe0
children
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rev   line source
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9db3e299b1c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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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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13
2
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14 @COLUMN_SELECT@
0
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16 @CMDLN_SQL_FILTER_FILTER_OPTION@
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18 #if int($min_kindreds) > 0:
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19 --min-kindreds $min_kindreds
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20 #end if
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22 #if str($families).strip():
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23 --families "$families"
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24 #end if
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26 $lenient
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27 $allow_unaffected
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30 -d $d
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32 #if int($min_gq) > 0:
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33 --min-gq $min_gq
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34 #end if
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36 #if int($gt_pl_max) > -1:
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37 --gt-pl-max $gt_pl_max
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38 #end if
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41 "${ infile }"
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42 > "${ outfile }"
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43 ]]>
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44 </command>
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45 <inputs>
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46 <expand macro="infile" />
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47 <expand macro="column_filter" />
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48 <expand macro="filter" />
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49 <expand macro="min_kindreds" />
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50 <expand macro="family" />
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51 <expand macro="lenient" />
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52 <expand macro="unaffected" />
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53 <expand macro="min_sequence_depth" />
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54 <expand macro="min_gq" />
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55 <expand macro="gt_pl_max" />
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56 </inputs>
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57 <outputs>
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58 <data name="outfile" format="tabular" />
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
4
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63 <conditional name="report">
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64 <param name="report_selector" value="column_filter" />
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65 <param name="columns" value="gene,ref,alt,impact" />
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66 </conditional>
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67 <output name="outfile">
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68 <assert_contents>
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69 <has_line_matching expression="gene&#009;ref&#009;alt&#009;impact.*" />
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70 </assert_contents>
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71 </output>
0
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72 </test>
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73 </tests>
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74 <help>
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75 **What it does**
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76
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77 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI,
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78 you can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring.
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79
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80 </help>
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81 <expand macro="citations"/>
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82 </tool>