Mercurial > repos > iuc > gemini_query

annotate gemini_query.xml @ 11:81db0d6200da draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 14:59:02 +0000
parents 37e2ac64e4f6
children
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11
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2">
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2 <description>Querying the GEMINI database</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">query</token>
7
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7
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8 <xml name="sorting">
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9 <param name="order_by" type="text"
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10 label="Sort the output by the following column(s)"
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11 help="" />
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12 <param name="sort_order" type="select" label="Sort order">
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13 <option value=" ASC">Ascending</option>
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14 <option value=" DESC">Descending</option>
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15 </param>
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16 </xml>
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17 <xml name="pheno_strat">
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18 <param name="phenotype" type="text"
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19 label="Phenotype to stratify samples across"
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20 help="Leave blank to stratify across the default phenotype column" />
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21 </xml>
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22 <xml name="sample_delimiter" token_applied_to="samples">
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23 <param argument="--sample-delim" name="sample_delim" type="text" value=","
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24 label="Delimiter to use in the list of affected @APPLIED_TO@"
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25 help="" />
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26 </xml>
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27 <xml name="dgidb_query">
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28 <param argument="--dgidb" name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False"
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29 label="Request drug-gene interaction info from DGIdb" help="" />
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30 </xml>
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31 <xml name="maf_extra_info">
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32 <param name="tumor_sample_name" type="text"
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33 label="Name of the tumor sample in the (multi-sample) GEMINI database"
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34 help="Specify only if the tumor sample is not the only sample in the database." />
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35 <param name="normal_sample_name" type="text"
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36 label="Name of the normal sample in the GEMINI database (for matched tumor/normal sample pair analyses only)" />
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37 </xml>
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38 </macros>
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39 <expand macro="requirements" />
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40 <expand macro="stdio" />
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41 <expand macro="version_command" />
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42 <command>
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43 <![CDATA[
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44 gemini @BINARY@
7
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45 ${query.oformat.report.header}
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46 ${query.oformat.report.dgidb}
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47
7
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48 #for $i in $query.filter_by_genotype:
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49 #set $multiline_sql_expr = str($i.gt_filter)
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50 #set $cmdln_param = "--gt-filter"
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51 @MULTILN_SQL_EXPR_TO_CMDLN@
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52 #end for
0
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53
7
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54 #for $i in $query.filter_by_sample:
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55 $i.family_wise
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56 #if int($i.min_kindreds) > 0:
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57 --min-kindreds ${i.min_kindreds}
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58 #end if
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59 ${i.in}
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60 #set $multiline_sql_expr = str($i.sample_filter)
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61 #set $cmdln_param = "--sample-filter"
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62 @MULTILN_SQL_EXPR_TO_CMDLN@
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63 #end for
0
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64
7
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65 #if str($query.oformat.report.format) == 'with_samples':
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66 #set $sample_delim = str($query.oformat.report.sample_delim) or ','
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67 --show-samples --sample-delim '$sample_delim'
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68 #elif str($query.oformat.report.format) == 'with_samples_flattened':
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69 --show-samples --format sampledetail
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70 #elif str($query.oformat.report.format) == 'with_families':
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71 #set $sample_delim = str($query.oformat.report.sample_delim) or ','
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72 --show-families --sample-delim '$sample_delim'
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73 #elif str($query.oformat.report.format) == 'carrier_summary':
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74 --carrier-summary-by-phenotype
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75 #if str($query.oformat.report.phenotype).strip():
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76 '${query.oformat.report.phenotype}'
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77 #else:
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78 affected
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79 #end if
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80 #elif str($query.oformat.report.format) != 'maf':
7
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81 --format ${query.oformat.report.format}
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82 #end if
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83
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84 #if str($query.interface) == 'basic':
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85 ## build the SQL query string from its components
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86 #if str($query.oformat.report.format) in ('vcf', 'tped'):
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87 #set $cols = "*"
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88 #elif str($query.oformat.report.format) == 'maf':
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89 #if str($query.oformat.report.tumor_sample_name):
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90 #set $gt_string = 'gt_alt_depths.{0}, gt_ref_depths.{0}, gts.{0}'.format(str($query.oformat.report.tumor_sample_name))
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91 #if str($query.oformat.report.normal_sample_name):
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92 #set $gt_string = $gt_string + ', gt_alt_depths.{0}, gt_ref_depths.{0}, gts.{0}'.format(str($query.oformat.report.normal_sample_name))
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93 #end if
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94 #else:
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95 #set $gt_string = '(gt_alt_depths).(*), (gt_ref_depths).(*), (gts).(*)'
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96 #end if
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97 #if str($query.oformat.report.mutation_status.status_select) == 'custom':
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98 ## Need to quote the user-specified mutation status for the SQL query
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99 #set $mutation_status = '"%s"' % str($query.oformat.report.mutation_status.status_custom)
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100 #elif str($query.oformat.report.mutation_status.status_select) == 'expression':
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101 ## For custom expressions, it is up to the user to ensure valid syntax
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102 #set $mutation_status = str($query.oformat.report.mutation_status.status_expression)
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103 #else:
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104 ## The user selected a fixed value from the list, but
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105 ## it still needs quoting.
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106 #set $mutation_status = '"%s"' % str($query.oformat.report.mutation_status.status_select)
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107 #end if
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108 #set $cols = 'ifnull(g1.gene, "unknown") AS Hugo_Symbol, ifnull(ifnull(g2.entrez_id, g1.entrez_id), "") AS Entrez_Gene_Id, "" AS Center, "37" AS NCBI_Build, replace(v.chrom, "chr", "") AS Chromosome, v.start + 1 AS Start_Position, v.end AS End_Position, "" as Strand, v.impact_so AS Variant_Classification, ifnull(nullif(v.type, "indel"), v.sub_type) AS Variant_Type, v.ref AS Reference_Allele, "${tumor_seq_allele1}" AS Tumor_Seq_Allele1, "${tumor_seq_allele2}" AS Tumor_Seq_Allele2, ifnull(v.rs_ids, ifnull(nullif(ifnull(nullif(v.in_omim = 0 AND v.cosmic_ids IS NULL AND v.max_aaf_all = -1, 1), "novel"), 0), "")) AS dbSNP_RS, "" AS dbSNP_Val_Status, printf("%s", "' + str($query.oformat.report.tumor_sample_id) + '") AS Tumor_Sample_Barcode, printf("%s", "' + str($query.oformat.report.norm_sample_id) + '") AS Matched_Norm_Sample_Barcode, "${match_norm_seq_allele1}" AS Match_Norm_Seq_Allele1, "${match_norm_seq_allele2}" AS Match_Norm_Seq_Allele2, "" AS Tumor_Validation_Allele1, "" AS Tumor_Validation_Allele2, "" AS Match_Norm_Validation_Allele1, "" AS Match_Norm_Validation_Allele2, "" AS Verification_Status, "" AS Validation_Status, ' + $mutation_status + ' AS Mutation_Status, "" AS Sequencing_Phase, "" AS Sequence_Source, "" AS Validation_Method, "" AS Score, "" AS BAM_File, "" AS Sequencer, ifnull(nullif(v.aa_change, ""), "p.=") AS HGVSp_Short, "${t_alt_count}" AS t_alt_count, "${t_ref_count}" AS t_ref_count, "${n_alt_count}" AS n_alt_count, "${n_ref_count}" AS n_ref_count, v.alt, ' + $gt_string
7
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109 #else:
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110 #set $report = $query.oformat.report.report
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111 @SET_COLS@
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112 #end if
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113 #set $q = "SELECT %s FROM variants" % $cols
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114 #if str($query.oformat.report.format) == 'maf':
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115 #set $q = $q + ' v LEFT JOIN (SELECT DISTINCT gene, is_hgnc, hgnc_id, entrez_id, chrom FROM gene_detailed) g1 ON v.gene = g1.gene AND v.chrom = g1.chrom LEFT JOIN (SELECT DISTINCT gene, is_hgnc, hgnc_id, entrez_id, transcript, chrom, ensembl_gene_id FROM gene_detailed) g2 ON g1.gene = g2.gene AND (v.transcript = g2.transcript OR v.transcript=g2.ensembl_gene_id)'
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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116 #end if
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117
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118 #set $where_clause_elements = []
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119 #if str($query.filter).strip():
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120 #silent $where_clause_elements.append(str($query.filter).strip())
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121 #end if
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122
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123 #set $regions = $query.regions
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124 @PARSE_REGION_ELEMENTS@
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125 #if $region_elements:
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126 #silent $where_clause_elements.append(" OR ".join($region_elements))
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127 #end if
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128 #if $where_clause_elements:
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129 #set $q = $q + " WHERE " + " AND ".join($where_clause_elements)
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130 #end if
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131 #if str($query.oformat.report.format) == 'maf':
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132 #set $q = $q + " GROUP BY v.variant_id"
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133 #end if
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134 #if str($query.oformat.report.order_by).strip():
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135 #set $q = $q + " ORDER BY " + str($query.oformat.report.order_by).strip() + str($query.oformat.report.sort_order)
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136 #end if
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137 #else
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138 ## The user entered the SQL query string directly.
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139 #set $q = str($query.q)
0
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140 #end if
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141
3
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142 #set $multiline_sql_expr = $q
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143 #set $cmdln_param = "-q"
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144 @MULTILN_SQL_EXPR_TO_CMDLN@
0
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145
7
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146 '$infile'
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147 #if str($query.oformat.report.format) == 'maf':
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148 > temp.txt && python '$__tool_directory__/gemini_mafify.py' temp.txt '${query.oformat.report.tumor_sample_name}' '${query.oformat.report.normal_sample_name}'
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149 #end if
7
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150 > '$outfile'
0
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151 ]]>
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152 </command>
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153 <inputs>
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154 <expand macro="infile" />
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155 <conditional name="query">
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156 <param name="interface" type="select"
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157 label="Build GEMINI query using"
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158 help="">
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159 <option value="basic">Basic variant query constructor</option>
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160 <option value="advanced">Advanced query constructor</option>
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161 </param>
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162 <when value="basic">
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163 <expand macro="gt_filter" />
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164 <expand macro="sample_filter" />
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165 <expand macro="region_filter" />
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166 <expand macro="filter" argument="" />
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167 <section name="oformat" title="Output format options" expanded="true">
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168 <conditional name="report">
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169 <param name="format" type="select"
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170 label="Type of report to generate">
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171 <option value="default">tabular (GEMINI default)</option>
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172 <option value="with_samples">tabular with affected samples</option>
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173 <option value="with_samples_flattened">tabular with affected samples flattened</option>
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174 <option value="with_families">tabular with affected families</option>
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175 <option value="carrier_summary">tabular with carrier summary</option>
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176 <option value="vcf">VCF (simplified)</option>
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177 <option value="json">JSON</option>
9
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178 <option value="maf">MAF (cBioportal-compatible)</option>
7
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179 <option value="tped">TPED</option>
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180 </param>
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181 <when value="default">
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182 <expand macro="add_header_column" />
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183 <expand macro="column_filter"
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184 minimalset="chrom, start, end, ref, alt, gene, impact"
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185 help=""/>
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186 <expand macro="dgidb_query" />
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187 <expand macro="sorting" />
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188 </when>
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189 <when value="with_samples">
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190 <expand macro="add_header_column" />
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191 <expand macro="sample_delimiter" />
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diff changeset
192 <expand macro="column_filter"
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193 minimalset="chrom, start, end, ref, alt, gene, impact"
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194 help=""/>
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195 <expand macro="dgidb_query" />
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196 <expand macro="sorting" />
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197 </when>
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198 <when value="with_samples_flattened">
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199 <expand macro="add_header_column" />
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200 <expand macro="column_filter"
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201 minimalset="chrom, start, end, ref, alt, gene, impact"
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202 help=""/>
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203 <param name="dgidb" type="hidden" value="" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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204 <expand macro="sorting" />
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205 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
206 <when value="with_families">
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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207 <expand macro="add_header_column" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
208 <expand macro="sample_delimiter" applied_to="families"/>
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209 <expand macro="column_filter"
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diff changeset
210 minimalset="chrom, start, end, ref, alt, gene, impact"
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diff changeset
211 help=""/>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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212 <expand macro="dgidb_query" />
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213 <expand macro="sorting" />
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214 </when>
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215 <when value="carrier_summary">
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216 <expand macro="add_header_column" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
217 <expand macro="pheno_strat" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
218 <expand macro="column_filter"
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diff changeset
219 minimalset="chrom, start, end, ref, alt, gene, impact"
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diff changeset
220 help=""/>
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diff changeset
221 <expand macro="dgidb_query" />
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222 <expand macro="sorting" />
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223 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
224 <when value="vcf">
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diff changeset
225 <expand macro="add_header_column" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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226 <param name="order_by" type="hidden" value="" />
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227 <param name="dgidb" type="hidden" value="" />
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228 </when>
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229 <when value="json">
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230 <param name="header" type="hidden" value="" />
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diff changeset
231 <expand macro="column_filter"
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diff changeset
232 minimalset="chrom, start, end, ref, alt, gene, impact"
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233 help=""/>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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234 <param name="dgidb" type="hidden" value="" />
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235 <expand macro="sorting" />
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236 </when>
9
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237 <when value="maf">
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238 <param name="header" type="hidden" value="--header" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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239 <param name="dgidb" type="hidden" value="" />
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240 <expand macro="maf_extra_info" />
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241 <param name="tumor_sample_id" type="text"
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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242 label="Tumor sample ID">
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243 <validator type="expression" message="A tumor sample identifier is required">value.strip()</validator>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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244 </param>
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245 <param name="norm_sample_id" type="text"
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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246 label="Normal sample ID (for matched tumor/normal sample pair analyses only)" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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247 <conditional name="mutation_status">
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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248 <param name="status_select" type="select"
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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249 label="Mutation status to be recorded for variants reported with this query"
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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250 help="'Somatic', 'Germline', 'LOH', 'Wildtype' and 'None' are fixed values that are treated explicitly by cBioportal. In particular, 'Somatic' and 'Germline' are supported by the cBioportal user interface in the Mutations tab, while 'LOH', 'Wildtype' and 'None' will not be loaded. Any other values will cause the variants to be loaded into cBioPortal and will be displayed as text in the Mutations tab.">
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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251 <option value="expression">Calculate per variant</option>
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252 <option value="custom">Other fixed value</option>
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253 <option value="Somatic" selected="true">Somatic</option>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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254 <option value="Germline">Germline</option>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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255 <option value="LOH">LOH</option>
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256 <option value="Wildtype">Wildtype</option>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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257 <option value="None">None</option>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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258 </param>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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259 <when value="Somatic" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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260 <when value="Germline" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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261 <when value="LOH" />
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262 <when value="Wildtype" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
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263 <when value="None" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
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264 <when value="custom">
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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265 <param name="status_custom" type="text"
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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266 label="Mutation status (custom value)">
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267 <validator type="expression" message="Need a value for Mutation status">value.strip()</validator>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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268 </param>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
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269 </when>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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270 <when value="expression">
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parents: 7
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271 <param name="status_expression" type="text"
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
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272 label="SQL expression used to compute per-variant status"
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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273 help="Enter a valid SQL result column expression to compute the mutation status from columns of the variants table in the GEMINI database. As one example, the expression ifnull(nullif(ifnull(nullif(ifnull(nullif(somatic_status, 3), 'LOH'), 2), 'Somatic'), 1), 'Germline') assumes that you have a column somatic_status added to the variants table of your database, and will record 'Germline', 'Somatic', or 'LOH' for variants with a value of 1, 2, or 3 in that column, respectively.">
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
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274 <expand macro="sanitize_query" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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275 <validator type="expression" message="Mutation status expression cannot be empty">value.strip()</validator>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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276 </param>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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277 </when>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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278 </conditional>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
diff changeset
279 <expand macro="sorting" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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280 </when>
7
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281 <when value="tped">
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282 <param name="header" type="hidden" value="" />
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283 <param name="dgidb" type="hidden" value="" />
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parents: 6
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284 <expand macro="sorting" />
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285 </when>
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286 </conditional>
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287 </section>
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288 </when>
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289 <when value="advanced">
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290 <param argument="-q" name="q" type="text" area="True" size="5x50"
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291 label="The query to be issued to the database"
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292 help="Formulate your query using SQL syntax.">
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293 <expand macro="sanitize_query" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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294 <validator type="expression" message="Query cannot be empty">value.strip()</validator>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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295 </param>
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296 <expand macro="gt_filter" />
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297 <expand macro="sample_filter" />
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298 <section name="oformat" title="Output format options" expanded="true">
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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299 <conditional name="report">
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300 <param name="format" type="select"
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301 label="Type of report to generate">
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302 <option value="default">tabular (GEMINI default)</option>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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303 <option value="with_samples">tabular with affected samples</option>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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304 <option value="with_samples_flattened">tabular with affected samples flattened</option>
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305 <option value="with_families">tabular with affected families</option>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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306 <option value="carrier_summary">tabular with carrier summary</option>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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307 <option value="vcf">VCF (simplified)</option>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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308 <option value="json">JSON</option>
9
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309 <option value="maf">MAF (cBioportal-compatible)</option>
7
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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310 <option value="tped">TPED</option>
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311 </param>
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312 <when value="default">
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313 <expand macro="add_header_column" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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314 <expand macro="dgidb_query" />
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315 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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316 <when value="with_samples">
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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317 <expand macro="add_header_column" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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318 <expand macro="sample_delimiter" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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319 <expand macro="dgidb_query" />
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320 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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321 <when value="with_samples_flattened">
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322 <expand macro="add_header_column" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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323 <param name="dgidb" type="hidden" value="" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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324 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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325 <when value="with_families">
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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326 <expand macro="add_header_column" />
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diff changeset
327 <expand macro="sample_delimiter" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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328 <expand macro="dgidb_query" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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329 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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330 <when value="carrier_summary">
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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331 <expand macro="pheno_strat" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
332 <expand macro="add_header_column" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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333 <expand macro="dgidb_query" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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334 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
335 <when value="vcf">
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
336 <expand macro="add_header_column" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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337 <param name="dgidb" type="hidden" value="" />
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338 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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339 <when value="json">
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340 <param name="header" type="hidden" value="" />
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341 <param name="dgidb" type="hidden" value="" />
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342 </when>
9
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343 <when value="maf">
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344 <param name="header" type="hidden" value="--header" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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345 <param name="dgidb" type="hidden" value="" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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346 <expand macro="maf_extra_info" />
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347 </when>
7
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348 <when value="tped">
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349 <param name="header" type="hidden" value="" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
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350 <param name="dgidb" type="hidden" value="" />
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351 </when>
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352 </conditional>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
353 </section>
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354 </when>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
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355 </conditional>
0
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iuc
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diff changeset
356 </inputs>
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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357 <outputs>
7
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iuc
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358 <data name="outfile" format="tabular">
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parents: 6
diff changeset
359 <change_format>
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parents: 6
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360 <when input="query.oformat.report.format" value="json" format="json" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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361 <when input="query.oformat.report.format" value="vcf" format="vcf" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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362 </change_format>
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
363 </data>
0
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
iuc
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diff changeset
364 </outputs>
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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diff changeset
365 <tests>
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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366 <test>
5
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367 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
7
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
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368 <conditional name="query">
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369 <param name="interface" value="advanced" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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370 <param name="q" value="select chrom,start from variants limit 10" />
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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371 </conditional>
5
1f5c3a55dfbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 4
diff changeset
372 <output name="outfile">
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parents: 4
diff changeset
373 <assert_contents>
1f5c3a55dfbb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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parents: 4
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374 <has_line_matching expression="chrom&#009;start" />
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375 </assert_contents>
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iuc
parents: 4
diff changeset
376 </output>
0
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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377 </test>
9
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
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378 <test>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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379 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
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380 <conditional name="query">
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
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381 <param name="interface" value="basic" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
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382 </conditional>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
diff changeset
383 <section name="oformat">
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
diff changeset
384 <conditional name="report">
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
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385 <param name="format" value="maf" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 7
diff changeset
386 <param name="tumor_sample_id" value="test" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
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387 </conditional>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
diff changeset
388 </section>
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
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389 <output name="outfile" file="gemini_query_as_maf_result.tabular" />
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 7
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390 </test>
11
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iuc
parents: 10
diff changeset
391 <test>
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iuc
parents: 10
diff changeset
392 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
81db0d6200da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
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parents: 10
diff changeset
393 <conditional name="query">
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iuc
parents: 10
diff changeset
394 <param name="interface" value="basic" />
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iuc
parents: 10
diff changeset
395 <repeat name="regions">
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parents: 10
diff changeset
396 <param name="chrom" value="chr1"/>
81db0d6200da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
iuc
parents: 10
diff changeset
397 <param name="start" value="0"/>
81db0d6200da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
iuc
parents: 10
diff changeset
398 <param name="end" value="13327"/>
81db0d6200da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
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parents: 10
diff changeset
399 </repeat>
81db0d6200da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
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parents: 10
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400 </conditional>
81db0d6200da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
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parents: 10
diff changeset
401 <output name="outfile" file="gemini_region_filter.tabular" />
81db0d6200da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
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parents: 10
diff changeset
402 </test>
0
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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diff changeset
403 </tests>
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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parents:
diff changeset
404 <help>
2
9dc6c42486a1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents: 0
diff changeset
405 <![CDATA[
0
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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diff changeset
406 **What it does**
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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407
7
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408 The real power in the GEMINI framework lies in the fact that all of your
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
409 genetic variants have been stored in a convenient database in the context of a
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
410 wealth of genome annotations that facilitate variant interpretation.
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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411 The expressive power of SQL allows one to pose intricate questions of one’s
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
412 variation data. This tool offers you a flexible, yet relatively easy way
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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413 to query your variants!
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
414
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
415 -----
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
416
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
417 *Building your variant query with the Basic variant query constructor*
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
418
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
419 This mode tries to break down the complexity of formulating GEMINI queries
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
420 into more easily digestable parts. In this mode, the tool also prevents you
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
421 from combining options that are incompatible or not meaningful.
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
422
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
423 *Genotype filters*
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
424
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
425 These are discussed `here
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
426 <https://gemini.readthedocs.io/en/latest/content/querying.html#gt-filter-filtering-on-genotypes>`__
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
427 in the GEMINI documentation.
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
428
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
429 The tool supports regular genotype filters like::
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
430
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
431 gt.sample1 == HET and gt_depths.sample1 >= 15
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
432
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
433 , which would keep only variants for which sample 1 is a heterozygous carrier
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
434 and if the genomic position in sample1 is covered by at least 15 sequencing
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
435 reads, as well as GEMINI wildcard filters of the general form
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
436 *(COLUMN).(SAMPLE_FILTER).(RULE).(RULE_ENFORCEMENT)* like::
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
437
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 6
diff changeset
438 (gt_types).(phenotype==2).(!=HOM_REF).(all)
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439
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440 , which keeps only variants for which all phenotypic samples are homozygous.
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441
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442 *Sample filters*
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443
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444 Sample filters have the same format as the second component of the genotype
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445 wildcard filters above, so::
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446
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447 phenotype == 2
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448
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449 would filter for phenotypically affected samples. In this case, however, the
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450 filter determines, from which samples variants should be reported, i.e., here,
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451 only variants found in phenotypically affected samples become analyzed. You can
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452 use the ``--in`` filter to adjust the exact meaning of the sample filter.
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453
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454 *Region filters*
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455
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456 They let you restrict your analysis to parts of the genome, which can be useful
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457 if you have prior knowledge of the approximate location of a variant of
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458 interest.
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459
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460 If you specify more then one region filter, they get combined with a logical
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461 *OR*, meaning variants and genes falling in *any* of the regions are reported.
0
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462
7
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463 *Additional constraints on variants*
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464
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465 These get translated directly into the WHERE clause of an SQL query and, thus,
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466 have to be expressed in valid SQL syntax. As an example you could use::
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467
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468 is_exonic = 1 and impact_severity != 'LOW'
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469
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470 to indicate that you are only interested in exonic variants that are not of
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471 *LOW* impact severity, *i.e.*, not silent mutations.
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472
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473 Note that in SQL syntax tests for equality use a single ``=``, while genotype
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474 filters (discussed above) are following Python syntax and use ``==`` for the
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475 same purpose. Also note that non-numerical values need to be enclosed in
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476 single-quotes, *e.g.* ``'LOW'``, but numerical values must *NOT* be.
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477
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478 -----
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479
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480 *Building your query with the Advanced query constructor*
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481
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482 For the sake of simplicity, the basic mode of the tool limits your queries to
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483 the variants table of the underlying database. While this still allows many
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484 useful queries to be formulated, it prevents you from joining information from
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485 other tables (in particular, the gene_detailed table) or to query a different
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486 table directly.
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487
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488 In advanced mode, you take responsibility for formulating the complete SQL
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489 query in correct syntax, which allows you to do anything you could do with the
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490 command line tool. Beyond querying other tables, this includes changing output
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491 column names, deriving simple statistics on columns using the SQL Min, Max,
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492 Count, Avg and Sum functions, and more.
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493
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494 The price you pay for this extra flexibility is that you will have to make sure
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495 that any other tool options you set are compatible with the result of your
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496 particular query. For example, most output formats except the tabular default
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497 output of GEMINI are incompatible with non-standard queries. Choosing
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498 non-compatible options can result in them getting ignored silently, but also
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499 in tool errors, or in problems with downstream tools.
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500
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501 The chapter `Querying the GEMINI database
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502 <http://gemini.readthedocs.org/en/latest/content/querying.html>`__ of the
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503 GEMINI documentation can get you started with formulating your own queries.
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504
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505 Note that genotype filters and sample filters cannot be expressed as genuine
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506 SQL queries, so even the Advanced query constructor is offering them. Region
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507 filters and sort order of rows and columns on the other hand can be controlled
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508 through SQL queries, like in this example::
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509
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510 SELECT gene, chrom, start, end, ref, alt FROM variants WHERE chrom = 'chr1'
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511 AND start >= 10000000 and stop <= 20000000 and is_lof = 1 ORDER BY chrom,
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512 start
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513
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514 , which would report all loss-of-function variants between 10,000,000 and
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515 20,000,000 on chr1 and report the selected columns sorted on chromosome, then
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516 position.
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517
2
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518 ]]>
0
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519 </help>
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520 <expand macro="citations"/>
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521 </tool>