Mercurial > repos > iuc > gemini_query

annotate gemini_query.xml @ 6:840fb4850be3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"
author iuc
date Fri, 24 Jan 2020 17:31:00 -0500
parents cd00221d67cb
children da74170c55c7
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5
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Querying the GEMINI database</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@">query</token>
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6
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7 <xml name="sorting">
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8 <param name="order_by" type="text"
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9 label="Sort the output by the following column(s)"
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10 help="" />
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11 <param name="sort_order" type="select" label="Sort order">
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12 <option value=" ASC">Ascending</option>
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13 <option value=" DESC">Descending</option>
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14 </param>
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15 </xml>
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16 <xml name="pheno_strat">
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17 <param name="phenotype" type="text"
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18 label="Phenotype to stratify samples across"
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19 help="Leave blank to stratify across the default phenotype column" />
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20 </xml>
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21 <xml name="sample_delimiter" token_applied_to="samples">
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22 <param argument="--sample-delim" name="sample_delim" type="text" value=","
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23 label="Delimiter to use in the list of affected @APPLIED_TO@"
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24 help="" />
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25 </xml>
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26 <xml name="dgidb_query">
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27 <param argument="--dgidb" name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"
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28 label="Request drug-gene interaction info from DGIdb" help="" />
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29 </xml>
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30 </macros>
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31 <expand macro="requirements" />
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32 <expand macro="stdio" />
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33 <expand macro="version_command" />
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34 <command>
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35 <![CDATA[
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36 gemini @BINARY@
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37 ${query.oformat.report.header}
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38 ${query.oformat.report.dgidb}
0
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39
5
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40 #for $i in $query.filter_by_genotype:
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41 #set $multiline_sql_expr = str($i.gt_filter)
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42 #set $cmdln_param = "--gt-filter"
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43 @MULTILN_SQL_EXPR_TO_CMDLN@
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44 #end for
0
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45
5
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46 #for $i in $query.filter_by_sample:
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47 $i.family_wise
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48 #if int($i.min_kindreds) > 0:
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49 --min-kindreds ${i.min_kindreds}
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50 #end if
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51 ${i.in}
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52 #set $multiline_sql_expr = str($i.sample_filter)
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53 #set $cmdln_param = "--sample-filter"
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54 @MULTILN_SQL_EXPR_TO_CMDLN@
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55 #end for
0
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56
5
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57 #if str($query.oformat.report.format) == 'with_samples':
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58 #set $sample_delim = str($query.oformat.report.sample_delim) or ','
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59 --show-samples --sample-delim '$sample_delim'
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60 #elif str($query.oformat.report.format) == 'with_samples_flattened':
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61 --show-samples --format sampledetail
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62 #elif str($query.oformat.report.format) == 'with_families':
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63 #set $sample_delim = str($query.oformat.report.sample_delim) or ','
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64 --show-families --sample-delim '$sample_delim'
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65 #elif str($query.oformat.report.format) == 'carrier_summary':
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66 --carrier-summary-by-phenotype
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67 #if str($query.oformat.report.phenotype).strip():
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68 '${query.oformat.report.phenotype}'
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69 #else:
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70 affected
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71 #end if
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72 #else:
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73 --format ${query.oformat.report.format}
0
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74 #end if
5
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75
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76 #if str($query.interface) == 'basic':
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77 ## build the SQL query string from its components
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78 #if str($query.oformat.report.format) in ('vcf', 'tped'):
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79 #set $cols = "*"
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80 #else:
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81 #set $report = $query.oformat.report.report
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82 @SET_COLS@
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83 #end if
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84 #set $q = "SELECT %s FROM variants" % $cols
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85 #set $where_clause_elements = []
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86 #if str($query.filter).strip():
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87 #silent $where_clause_elements.append(str($query.filter).strip())
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88 #end if
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89
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90 #set $regions = $query.regions
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91 @PARSE_REGION_ELEMENTS@
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92 #if $region_elements:
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93 #silent $where_clause_elements.append(" OR ".join($region_elements))
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94 #end if
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95 #if $where_clause_elements:
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96 #set $q = $q + " WHERE " + " AND ".join($where_clause_elements)
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97 #end if
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98 #if str($query.oformat.report.order_by).strip():
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99 #set $q = $q + " ORDER BY " + str($query.oformat.report.order_by).strip() + str($query.oformat.report.sort_order)
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100 #end if
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101 #else
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102 ## The user entered the SQL query string directly.
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103 #set $q = str($query.q)
0
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104 #end if
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105
3
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106 #set $multiline_sql_expr = $q
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107 #set $cmdln_param = "-q"
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108 @MULTILN_SQL_EXPR_TO_CMDLN@
0
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109
5
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110 '$infile'
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111 > '$outfile'
0
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112 ]]>
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113 </command>
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114 <inputs>
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115 <expand macro="infile" />
5
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116 <conditional name="query">
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117 <param name="interface" type="select"
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118 label="Build GEMINI query using"
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119 help="">
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120 <option value="basic">Basic variant query constructor</option>
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121 <option value="advanced">Advanced query constructor</option>
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122 </param>
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123 <when value="basic">
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124 <expand macro="gt_filter" />
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125 <expand macro="sample_filter" />
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126 <expand macro="region_filter" />
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127 <expand macro="filter" argument="" />
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128 <section name="oformat" title="Output format options" expanded="true">
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129 <conditional name="report">
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130 <param name="format" type="select"
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131 label="Type of report to generate">
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132 <option value="default">tabular (GEMINI default)</option>
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133 <option value="with_samples">tabular with affected samples</option>
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134 <option value="with_samples_flattened">tabular with affected samples flattened</option>
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135 <option value="with_families">tabular with affected families</option>
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136 <option value="carrier_summary">tabular with carrier summary</option>
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137 <option value="vcf">VCF (simplified)</option>
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138 <option value="json">JSON</option>
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139 <option value="tped">TPED</option>
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140 </param>
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141 <when value="default">
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142 <expand macro="add_header_column" />
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143 <expand macro="column_filter"
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144 minimalset="chrom, start, end, ref, alt, gene, impact"
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145 help=""/>
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146 <expand macro="dgidb_query" />
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147 <expand macro="sorting" />
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148 </when>
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149 <when value="with_samples">
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150 <expand macro="add_header_column" />
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151 <expand macro="sample_delimiter" />
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152 <expand macro="column_filter"
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153 minimalset="chrom, start, end, ref, alt, gene, impact"
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154 help=""/>
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155 <expand macro="dgidb_query" />
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156 <expand macro="sorting" />
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157 </when>
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158 <when value="with_samples_flattened">
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159 <expand macro="add_header_column" />
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160 <expand macro="column_filter"
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161 minimalset="chrom, start, end, ref, alt, gene, impact"
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162 help=""/>
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163 <param name="dgidb" type="hidden" value="" />
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164 <expand macro="sorting" />
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165 </when>
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166 <when value="with_families">
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167 <expand macro="add_header_column" />
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168 <expand macro="sample_delimiter" applied_to="families"/>
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169 <expand macro="column_filter"
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170 minimalset="chrom, start, end, ref, alt, gene, impact"
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171 help=""/>
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172 <expand macro="dgidb_query" />
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173 <expand macro="sorting" />
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174 </when>
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175 <when value="carrier_summary">
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176 <expand macro="add_header_column" />
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177 <expand macro="pheno_strat" />
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178 <expand macro="column_filter"
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179 minimalset="chrom, start, end, ref, alt, gene, impact"
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180 help=""/>
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181 <expand macro="dgidb_query" />
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182 <expand macro="sorting" />
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183 </when>
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184 <when value="vcf">
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185 <expand macro="add_header_column" />
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186 <param name="order_by" type="hidden" value="" />
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187 <param name="dgidb" type="hidden" value="" />
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188 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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189 <when value="json">
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190 <param name="header" type="hidden" value="" />
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191 <expand macro="column_filter"
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192 minimalset="chrom, start, end, ref, alt, gene, impact"
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193 help=""/>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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194 <param name="dgidb" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
195 <expand macro="sorting" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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196 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
197 <when value="tped">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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198 <param name="header" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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199 <param name="dgidb" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
200 <expand macro="sorting" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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201 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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202 </conditional>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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203 </section>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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204 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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205 <when value="advanced">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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206 <param argument="-q" name="q" type="text" area="True" size="5x50"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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207 label="The query to be issued to the database"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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208 help="Formulate your query using SQL syntax.">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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209 <expand macro="sanitize_query" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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210 <validator type="expression" message="Query cannot be empty">value.strip()</validator>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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211 </param>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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212 <expand macro="gt_filter" />
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213 <expand macro="sample_filter" />
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214 <section name="oformat" title="Output format options" expanded="true">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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215 <conditional name="report">
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216 <param name="format" type="select"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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217 label="Type of report to generate">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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218 <option value="default">tabular (GEMINI default)</option>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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219 <option value="with_samples">tabular with affected samples</option>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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220 <option value="with_samples_flattened">tabular with affected samples flattened</option>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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221 <option value="with_families">tabular with affected families</option>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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222 <option value="carrier_summary">tabular with carrier summary</option>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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223 <option value="vcf">VCF (simplified)</option>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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224 <option value="json">JSON</option>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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225 <option value="tped">TPED</option>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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226 </param>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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227 <when value="default">
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228 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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229 <expand macro="dgidb_query" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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230 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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231 <when value="with_samples">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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232 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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233 <expand macro="sample_delimiter" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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234 <expand macro="dgidb_query" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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235 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
236 <when value="with_samples_flattened">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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237 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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238 <param name="dgidb" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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239 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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240 <when value="with_families">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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241 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
242 <expand macro="sample_delimiter" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
243 <expand macro="dgidb_query" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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244 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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245 <when value="carrier_summary">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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246 <expand macro="pheno_strat" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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247 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
248 <expand macro="dgidb_query" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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249 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
250 <when value="vcf">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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251 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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252 <param name="dgidb" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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253 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
254 <when value="json">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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255 <param name="header" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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256 <param name="dgidb" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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257 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
258 <when value="tped">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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259 <param name="header" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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260 <param name="dgidb" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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261 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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262 </conditional>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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263 </section>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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264 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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265 </conditional>
0
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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266 </inputs>
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267 <outputs>
5
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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268 <data name="outfile" format="tabular">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
269 <change_format>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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270 <when input="query.oformat.report.format" value="json" format="json" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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271 <when input="query.oformat.report.format" value="vcf" format="vcf" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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272 </change_format>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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273 </data>
0
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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274 </outputs>
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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275 <tests>
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276 <test>
4
7ca6716748c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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277 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
5
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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278 <conditional name="query">
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279 <param name="interface" value="advanced" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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280 <param name="q" value="select chrom,start from variants limit 10" />
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281 </conditional>
4
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282 <output name="outfile">
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283 <assert_contents>
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284 <has_line_matching expression="chrom&#009;start" />
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285 </assert_contents>
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286 </output>
0
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287 </test>
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288 </tests>
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289 <help>
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290 <![CDATA[
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291 **What it does**
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292
5
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293 The real power in the GEMINI framework lies in the fact that all of your
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294 genetic variants have been stored in a convenient database in the context of a
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295 wealth of genome annotations that facilitate variant interpretation.
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296 The expressive power of SQL allows one to pose intricate questions of one’s
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297 variation data. This tool offers you a flexible, yet relatively easy way
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298 to query your variants!
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299
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300 -----
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301
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302 *Building your variant query with the Basic variant query constructor*
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303
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304 This mode tries to break down the complexity of formulating GEMINI queries
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305 into more easily digestable parts. In this mode, the tool also prevents you
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306 from combining options that are incompatible or not meaningful.
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307
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308 *Genotype filters*
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309
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310 These are discussed `here
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311 <https://gemini.readthedocs.io/en/latest/content/querying.html#gt-filter-filtering-on-genotypes>`__
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312 in the GEMINI documentation.
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313
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314 The tool supports regular genotype filters like::
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315
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316 gt.sample1 == HET and gt_depths.sample1 >= 15
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317
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318 , which would keep only variants for which sample 1 is a heterozygous carrier
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319 and if the genomic position in sample1 is covered by at least 15 sequencing
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320 reads, as well as GEMINI wildcard filters of the general form
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321 *(COLUMN).(SAMPLE_FILTER).(RULE).(RULE_ENFORCEMENT)* like::
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322
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323 (gt_types).(phenotype==2).(!=HOM_REF).(all)
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324
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325 , which keeps only variants for which all phenotypic samples are homozygous.
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326
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327 *Sample filters*
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328
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329 Sample filters have the same format as the second component of the genotype
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330 wildcard filters above, so::
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331
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332 phenotype == 2
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333
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334 would filter for phenotypically affected samples. In this case, however, the
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335 filter determines, from which samples variants should be reported, i.e., here,
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336 only variants found in phenotypically affected samples become analyzed. You can
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337 use the ``--in`` filter to adjust the exact meaning of the sample filter.
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338
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339 *Region filters*
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340
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341 They let you restrict your analysis to parts of the genome, which can be useful
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342 if you have prior knowledge of the approximate location of a variant of
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343 interest.
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344
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345 If you specify more then one region filter, they get combined with a logical
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346 *OR*, meaning variants and genes falling in *any* of the regions are reported.
0
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347
5
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348 *Additional constraints on variants*
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349
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350 These get translated directly into the WHERE clause of an SQL query and, thus,
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351 have to be expressed in valid SQL syntax. As an example you could use::
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352
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353 is_exonic = 1 and impact_severity != 'LOW'
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354
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355 to indicate that you are only interested in exonic variants that are not of
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356 *LOW* impact severity, *i.e.*, not silent mutations.
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357
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358 Note that in SQL syntax tests for equality use a single ``=``, while genotype
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359 filters (discussed above) are following Python syntax and use ``==`` for the
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360 same purpose. Also note that non-numerical values need to be enclosed in
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361 single-quotes, *e.g.* ``'LOW'``, but numerical values must *NOT* be.
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362
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363 -----
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364
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365 *Building your query with the Advanced query constructor*
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366
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367 For the sake of simplicity, the basic mode of the tool limits your queries to
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368 the variants table of the underlying database. While this still allows many
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369 useful queries to be formulated, it prevents you from joining information from
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370 other tables (in particular, the gene_detailed table) or to query a different
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371 table directly.
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372
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373 In advanced mode, you take responsibility for formulating the complete SQL
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374 query in correct syntax, which allows you to do anything you could do with the
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375 command line tool. Beyond querying other tables, this includes changing output
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376 column names, deriving simple statistics on columns using the SQL Min, Max,
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377 Count, Avg and Sum functions, and more.
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378
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379 The price you pay for this extra flexibility is that you will have to make sure
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380 that any other tool options you set are compatible with the result of your
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381 particular query. For example, most output formats except the tabular default
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382 output of GEMINI are incompatible with non-standard queries. Choosing
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383 non-compatible options can result in them getting ignored silently, but also
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384 in tool errors, or in problems with downstream tools.
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385
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386 The chapter `Querying the GEMINI database
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387 <http://gemini.readthedocs.org/en/latest/content/querying.html>`__ of the
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388 GEMINI documentation can get you started with formulating your own queries.
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389
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390 Note that genotype filters and sample filters cannot be expressed as genuine
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391 SQL queries, so even the Advanced query constructor is offering them. Region
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392 filters and sort order of rows and columns on the other hand can be controlled
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393 through SQL queries, like in this example::
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394
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395 SELECT gene, chrom, start, end, ref, alt FROM variants WHERE chrom = 'chr1'
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396 AND start >= 10000000 and stop <= 20000000 and is_lof = 1 ORDER BY chrom,
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397 start
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398
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399 , which would report all loss-of-function variants between 10,000,000 and
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400 20,000,000 on chr1 and report the selected columns sorted on chromosome, then
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401 position.
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402
0
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403 ]]>
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404 </help>
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405 <expand macro="citations"/>
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406 </tool>