Mercurial > repos > yusuf > combine_hgvs_annotations

annotate CombineHGVSAnnotations.xml @ 0:baf1543e8ae1 default tip

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initial commit
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:27:49 -0600
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1 <?xml version="1.0"?>
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2
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3 <tool id="hgvs_combine_1" name="Combine multiple HGVS tables">
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4 <description> to find concordant and discordant variant calls</description>
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5 <version_string>combine_hgvs_tables -v</version_string>
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6 <command interpreter="perl">combine_hgvs_tables -q $collapse $output_hgvs_table
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7 $params.input_hgvs_table_name1 $params.input_hgvs_table1
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8 $params.input_hgvs_table_name2 $params.input_hgvs_table2
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9 #if $int($str($params.source_select)) &gt; 2:
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10 $params.input_hgvs_table_name3 $params.input_hgvs_table3
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11 #end if
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12 #if $int($str($params.source_select)) &gt; 3:
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13 $params.input_hgvs_table_name4 $params.input_hgvs_table4
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14 #end if
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15 #if $int($str($params.source_select)) &gt; 4:
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16 $params.input_hgvs_table_name5 $params.input_hgvs_table5
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17 #end if
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18 #if $int($str($params.source_select)) &gt; 5:
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19 $params.input_hgvs_table_name6 $params.input_hgvs_table6
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20 #end if
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21 #if $int($str($params.source_select)) &gt; 6:
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22 $params.input_hgvs_table_name7 $params.input_hgvs_table7
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23 #end if
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24 #if $int($str($params.source_select)) &gt; 7:
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25 $params.input_hgvs_table_name8 $params.input_hgvs_table8
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26 #end if
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27 #if $int($str($params.source_select)) &gt; 8:
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28 $params.input_hgvs_table_name9 $params.input_hgvs_table9
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29 #end if
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30 </command>
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31 <inputs>
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32 <param name="collapse" type="boolean" truevalue="true" falsevalue="false" value="False" label="Collapse stats. If unchecked, column values for zygosity, quality, variant and total depth will have multiple values separated by ';'. If checked, each of these columns will be averaged out amongst input values to report a consensus."/>
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33 <conditional name="params">
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34 <param name="source_select" type="select" label="Number of variant call tables to combine">
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35 <option value="2" selected="true">2</option>
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36 <option value="3">3</option>
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37 <option value="4">4</option>
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38 <option value="5">5</option>
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39 <option value="6">6</option>
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40 <option value="7">7</option>
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41 <option value="8">8</option>
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42 <option value="9">9</option>
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43 </param>
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44 <when value="2">
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45 <param name="input_hgvs_table_name1" type="text" label="Dataset name to be reported in the output (e.g. GATK_calls or Patient001)"/>
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46 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
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47 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
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48 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
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49 </when>
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50 <when value="3">
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51 <param name="input_hgvs_table_name1" type="text" label="Dataset name to be reported in the output (e.g. GATK_calls or Patient001)"/>
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52 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
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53 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
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54 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
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55 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
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56 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
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57 </when>
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58 <when value="4">
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59 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
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60 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
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61 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
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62 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
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63 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
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64 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
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65 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
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66 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
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67 </when>
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68 <when value="5">
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69 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
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70 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
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71 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
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72 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
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73 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
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74 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
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75 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
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76 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
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77 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
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78 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
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79 </when>
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80 <when value="6">
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81 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
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82 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
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83 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
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84 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
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85 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
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86 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
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87 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
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88 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
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89 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
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90 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
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91 <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/>
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92 <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/>
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93 </when>
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94 <when value="7">
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95 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
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96 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
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97 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
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98 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
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99 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
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100 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
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101 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
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102 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
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103 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
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104 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
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105 <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/>
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106 <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/>
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107 <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/>
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108 <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/>
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109 </when>
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110 <when value="8">
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111 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
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112 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
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113 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
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114 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
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115 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
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116 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
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117 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
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118 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
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119 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
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120 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
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121 <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/>
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122 <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/>
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123 <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/>
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124 <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/>
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125 <param name="input_hgvs_table_name8" type="text" label="Dataset name #8"/>
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126 <param format="achri_snp_table" name="input_hgvs_table8" type="data" label="Eighth table"/>
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127 </when>
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128 <when value="9">
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129 <param name="input_hgvs_table_name1" type="text" label="Name to be reported in the output (e.g. GATK_calls or Patient0001)"/>
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130 <param format="achri_snp_table" name="input_hgvs_table1" type="data" label="First table (will be reported first in the output final column)"/>
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131 <param name="input_hgvs_table_name2" type="text" label="Dataset name to be reported in the output (e.g. LifeScope_calls or Patient002)"/>
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132 <param format="achri_snp_table" name="input_hgvs_table2" type="data" label="Second table (will be reported second in the output final column)"/>
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133 <param name="input_hgvs_table_name3" type="text" label="Dataset name #3"/>
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134 <param format="achri_snp_table" name="input_hgvs_table3" type="data" label="Third table"/>
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135 <param name="input_hgvs_table_name4" type="text" label="Dataset name #4"/>
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136 <param format="achri_snp_table" name="input_hgvs_table4" type="data" label="Fouth table"/>
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137 <param name="input_hgvs_table_name5" type="text" label="Dataset name #5"/>
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138 <param format="achri_snp_table" name="input_hgvs_table5" type="data" label="Fifth table"/>
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139 <param name="input_hgvs_table_name6" type="text" label="Dataset name #6"/>
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140 <param format="achri_snp_table" name="input_hgvs_table6" type="data" label="Sixth table"/>
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141 <param name="input_hgvs_table_name7" type="text" label="Dataset name #7"/>
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142 <param format="achri_snp_table" name="input_hgvs_table7" type="data" label="Seventh table"/>
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143 <param name="input_hgvs_table_name8" type="text" label="Dataset name #8"/>
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144 <param format="achri_snp_table" name="input_hgvs_table8" type="data" label="Eighth table"/>
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145 <param name="input_hgvs_table_name9" type="text" label="Dataset name #9"/>
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146 <param format="achri_snp_table" name="input_hgvs_table9" type="data" label="Nineth table"/>
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147 </when>
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148 </conditional>
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149 </inputs>
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150 <outputs>
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151 <data format="achri_snp_table" name="output_hgvs_table" type="data" label="HGVS variant table, combining multiple call sets"/>
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152 </outputs>
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153
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154 <tests>
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155 </tests>
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156
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157 <help>
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158 This tool takes multiple annotated HGVS variant tables and outputs a single table with an extra last column describing the list of input tables that reported the variant.
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159 This may be used to combine multiple variant predictions for the same sample (e.g. a frameshift detection tool and a SNP tool, or two SNP tools using different algorithms).
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160 It may also be used to highlight the concordance between individuals with similar phenotypes (common genetic cause), or isolate de novo mutations in a child (where trio data is available).</help>
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161
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162
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163 </tool>