Mercurial > repos > iuc > gemini_recessive_and_dominant

annotate gemini_autosomal_recessive.xml @ 4:05124dc72dba draft default tip

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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 12:43:22 -0500
parents 4086bb81f52a
children
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4
05124dc72dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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1 <tool id="gemini_recessive_and_dominant" name="GEMINI autosomal recessive/dominant" version="@VERSION@.1">
0
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2 <description>Find variants meeting an autosomal recessive/dominant model</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 gemini
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12
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13 #if str($rec_or_dom) == 'recessive':
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14 ## start autosomal_recessive
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15 autosomal_recessive
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16 #else:
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17 ## start autosomal_dominant
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18 autosomal_dominant
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19 #end if
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20
2
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21 @COLUMN_SELECT@
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23 @CMDLN_SQL_FILTER_FILTER_OPTION@
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25 -d $d
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26 #if int($min_kindreds) > 0:
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27 --min-kindreds $min_kindreds
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28 #end if
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30 #if str($families).strip():
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31 --families "$families"
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32 #end if
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33
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34 $lenient
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35 $allow_unaffected
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36
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37 #if int($min_gq) > 0:
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38 --min-gq $min_gq
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39 #end if
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40
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41 #if int($gt_pl_max) > -1:
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42 --gt-pl-max $gt_pl_max
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43 #end if
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44
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45 "${ infile }"
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46 > "${ outfile }"
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47 ]]>
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48 </command>
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49 <inputs>
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50
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51 <param name="rec_or_dom" type="select" label="Autosomal ..." help="">
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52 <option value="recessive">recessive</option>
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53 <option value="dominant">dominant</option>
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54 </param>
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55
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56 <expand macro="infile" />
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57 <expand macro="column_filter" />
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58 <expand macro="filter" />
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59 <expand macro="min_sequence_depth" />
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60 <expand macro="family" />
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61 <expand macro="lenient" />
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62 <expand macro="unaffected" />
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63 <expand macro="min_kindreds" />
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64 <expand macro="min_gq" />
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65 <expand macro="gt_pl_max" />
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66
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67 </inputs>
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68 <outputs>
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69 <data name="outfile" format="tabular" />
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70 </outputs>
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71 <tests>
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72 <test>
4
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73 <param name="infile" value="gemini_auto_dom_input.db" ftype="gemini.sqlite" />
0
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74 <param name="rec_or_dom" value="dominant" />
4
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75 <conditional name="report">
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76 <param name="report_selector" value="column_filter" />
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77 <param name="columns" value="gene,chrom,impact" />
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78 </conditional>
0
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79 <param name="lenient" value="true" />
4
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80 <output name="outfile">
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81 <assert_contents>
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82 <has_line_matching expression="gene&#009;chrom&#009;impact.*" />
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83 </assert_contents>
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84 </output>
0
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85 </test>
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86 <test>
4
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87 <param name="infile" value="gemini_auto_rec_input.db" ftype="gemini.sqlite" />
0
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88 <param name="rec_or_dom" value="recessive" />
4
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89 <conditional name="report">
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90 <param name="report_selector" value="column_filter" />
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91 <param name="columns" value="gene,chrom,impact" />
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92 </conditional>
0
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93 <param name="lenient" value="true" />
4
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94 <output name="outfile">
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95 <assert_contents>
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96 <has_line_matching expression="gene&#009;chrom&#009;impact.*" />
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97 </assert_contents>
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98 </output>
0
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99 </test>
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100 </tests>
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101 <help>
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102 **What it does**
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103
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104 Assuming you have defined the familial relationships between samples when loading your VCF into GEMINI, one can leverage a
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105 built-in tool for identifying variants that meet an autosomal recessive or dominant inheritance pattern.
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106 The reported variants will be restricted to those variants having the potential to impact the function of affecting protein coding transcripts.
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107
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108 </help>
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109 <expand macro="citations"/>
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110 </tool>