Mercurial > repos > iuc > gemini_query

annotate gemini_query.xml @ 7:da74170c55c7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
author iuc
date Tue, 10 Mar 2020 06:14:55 -0400
parents cd00221d67cb
children 77a1e60fd1de
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7
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy1">
0
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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>
5
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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 <xml name="maf_extra_info">
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31 <param name="tumor_sample_name" type="text"
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32 label="Name of the tumor sample in the (multi-sample) GEMINI database"
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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33 help="Specify only if the tumor sample is not the only sample in the database." />
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34 <param name="normal_sample_name" type="text"
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35 label="Name of the normal sample in the GEMINI database (for matched tumor/normal sample pair analyses only)" />
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36 </xml>
0
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37 </macros>
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38 <expand macro="requirements" />
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39 <expand macro="stdio" />
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40 <expand macro="version_command" />
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41 <command>
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42 <![CDATA[
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43 gemini @BINARY@
5
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44 ${query.oformat.report.header}
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45 ${query.oformat.report.dgidb}
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46
5
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47 #for $i in $query.filter_by_genotype:
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48 #set $multiline_sql_expr = str($i.gt_filter)
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49 #set $cmdln_param = "--gt-filter"
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50 @MULTILN_SQL_EXPR_TO_CMDLN@
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51 #end for
0
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52
5
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53 #for $i in $query.filter_by_sample:
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54 $i.family_wise
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55 #if int($i.min_kindreds) > 0:
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56 --min-kindreds ${i.min_kindreds}
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57 #end if
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58 ${i.in}
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59 #set $multiline_sql_expr = str($i.sample_filter)
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60 #set $cmdln_param = "--sample-filter"
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61 @MULTILN_SQL_EXPR_TO_CMDLN@
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62 #end for
0
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63
5
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64 #if str($query.oformat.report.format) == 'with_samples':
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65 #set $sample_delim = str($query.oformat.report.sample_delim) or ','
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66 --show-samples --sample-delim '$sample_delim'
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67 #elif str($query.oformat.report.format) == 'with_samples_flattened':
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68 --show-samples --format sampledetail
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69 #elif str($query.oformat.report.format) == 'with_families':
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70 #set $sample_delim = str($query.oformat.report.sample_delim) or ','
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71 --show-families --sample-delim '$sample_delim'
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72 #elif str($query.oformat.report.format) == 'carrier_summary':
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73 --carrier-summary-by-phenotype
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74 #if str($query.oformat.report.phenotype).strip():
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75 '${query.oformat.report.phenotype}'
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76 #else:
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77 affected
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78 #end if
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79 #elif str($query.oformat.report.format) != 'maf':
5
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80 --format ${query.oformat.report.format}
0
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81 #end if
5
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82
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83 #if str($query.interface) == 'basic':
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84 ## build the SQL query string from its components
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85 #if str($query.oformat.report.format) in ('vcf', 'tped'):
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86 #set $cols = "*"
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87 #elif str($query.oformat.report.format) == 'maf':
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88 #if str($query.oformat.report.tumor_sample_name):
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89 #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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90 #if str($query.oformat.report.normal_sample_name):
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91 #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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92 #end if
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93 #else:
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94 #set $gt_string = '(gt_alt_depths).(*), (gt_ref_depths).(*), (gts).(*)'
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95 #end if
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96 #if str($query.oformat.report.mutation_status.status_select) == 'custom':
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97 ## Need to quote the user-specified mutation status for the SQL query
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98 #set $mutation_status = '"%s"' % str($query.oformat.report.mutation_status.status_custom)
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99 #elif str($query.oformat.report.mutation_status.status_select) == 'expression':
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100 ## For custom expressions, it is up to the user to ensure valid syntax
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101 #set $mutation_status = str($query.oformat.report.mutation_status.status_expression)
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102 #else:
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103 ## The user selected a fixed value from the list, but
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104 ## it still needs quoting.
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105 #set $mutation_status = '"%s"' % str($query.oformat.report.mutation_status.status_select)
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106 #end if
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107 #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
5
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108 #else:
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109 #set $report = $query.oformat.report.report
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110 @SET_COLS@
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111 #end if
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112 #set $q = "SELECT %s FROM variants" % $cols
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113 #if str($query.oformat.report.format) == 'maf':
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114 #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)'
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115 #end if
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116
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117 #set $where_clause_elements = []
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118 #if str($query.filter).strip():
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119 #silent $where_clause_elements.append(str($query.filter).strip())
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120 #end if
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121
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122 #set $regions = $query.regions
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123 @PARSE_REGION_ELEMENTS@
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124 #if $region_elements:
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125 #silent $where_clause_elements.append(" OR ".join($region_elements))
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126 #end if
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127 #if $where_clause_elements:
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128 #set $q = $q + " WHERE " + " AND ".join($where_clause_elements)
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129 #end if
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130 #if str($query.oformat.report.format) == 'maf':
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131 #set $q = $q + " GROUP BY v.variant_id"
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132 #end if
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133 #if str($query.oformat.report.order_by).strip():
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134 #set $q = $q + " ORDER BY " + str($query.oformat.report.order_by).strip() + str($query.oformat.report.sort_order)
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135 #end if
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136 #else
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137 ## The user entered the SQL query string directly.
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138 #set $q = str($query.q)
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139 #end if
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140
3
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141 #set $multiline_sql_expr = $q
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142 #set $cmdln_param = "-q"
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143 @MULTILN_SQL_EXPR_TO_CMDLN@
0
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144
5
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145 '$infile'
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146 #if str($query.oformat.report.format) == 'maf':
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147 > temp.txt && python '$__tool_directory__/gemini_mafify.py' temp.txt '${query.oformat.report.tumor_sample_name}' '${query.oformat.report.normal_sample_name}'
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148 #end if
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149 > '$outfile'
0
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150 ]]>
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151 </command>
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152 <inputs>
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153 <expand macro="infile" />
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154 <conditional name="query">
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155 <param name="interface" type="select"
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156 label="Build GEMINI query using"
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157 help="">
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158 <option value="basic">Basic variant query constructor</option>
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159 <option value="advanced">Advanced query constructor</option>
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160 </param>
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161 <when value="basic">
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162 <expand macro="gt_filter" />
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163 <expand macro="sample_filter" />
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164 <expand macro="region_filter" />
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165 <expand macro="filter" argument="" />
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166 <section name="oformat" title="Output format options" expanded="true">
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167 <conditional name="report">
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168 <param name="format" type="select"
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169 label="Type of report to generate">
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170 <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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171 <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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diff changeset
172 <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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173 <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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174 <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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175 <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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176 <option value="json">JSON</option>
7
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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177 <option value="maf">MAF (cBioportal-compatible)</option>
5
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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178 <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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179 </param>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
180 <when value="default">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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181 <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
182 <expand macro="column_filter"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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183 minimalset="chrom, start, end, ref, alt, gene, impact"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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184 help=""/>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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185 <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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186 <expand macro="sorting" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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187 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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188 <when value="with_samples">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
189 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
190 <expand macro="sample_delimiter" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
191 <expand macro="column_filter"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
192 minimalset="chrom, start, end, ref, alt, gene, impact"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
193 help=""/>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
194 <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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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
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197 <when value="with_samples_flattened">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
198 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
199 <expand macro="column_filter"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
200 minimalset="chrom, start, end, ref, alt, gene, impact"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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201 help=""/>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
202 <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
203 <expand macro="sorting" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
204 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
205 <when value="with_families">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
206 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
207 <expand macro="sample_delimiter" applied_to="families"/>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
208 <expand macro="column_filter"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
209 minimalset="chrom, start, end, ref, alt, gene, impact"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
210 help=""/>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
211 <expand macro="dgidb_query" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
212 <expand macro="sorting" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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213 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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214 <when value="carrier_summary">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
215 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
216 <expand macro="pheno_strat" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
217 <expand macro="column_filter"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
218 minimalset="chrom, start, end, ref, alt, gene, impact"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
219 help=""/>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
220 <expand macro="dgidb_query" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
221 <expand macro="sorting" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 4
diff changeset
222 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
223 <when value="vcf">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
224 <expand macro="add_header_column" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
225 <param name="order_by" 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
226 <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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diff changeset
227 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
228 <when value="json">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
229 <param name="header" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
230 <expand macro="column_filter"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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diff changeset
231 minimalset="chrom, start, end, ref, alt, gene, impact"
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
232 help=""/>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
233 <param name="dgidb" type="hidden" value="" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
234 <expand macro="sorting" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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235 </when>
7
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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236 <when value="maf">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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237 <param name="header" type="hidden" value="--header" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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238 <param name="dgidb" type="hidden" value="" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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239 <expand macro="maf_extra_info" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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240 <param name="tumor_sample_id" type="text"
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 5
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241 label="Tumor sample ID">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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242 <validator type="expression" message="A tumor sample identifier is required">value.strip()</validator>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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diff changeset
243 </param>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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244 <param name="norm_sample_id" type="text"
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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245 label="Normal sample ID (for matched tumor/normal sample pair analyses only)" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 5
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246 <conditional name="mutation_status">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
247 <param name="status_select" type="select"
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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248 label="Mutation status to be recorded for variants reported with this query"
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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249 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.">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
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diff changeset
250 <option value="expression">Calculate per variant</option>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
251 <option value="custom">Other fixed value</option>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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252 <option value="Somatic" selected="true">Somatic</option>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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253 <option value="Germline">Germline</option>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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254 <option value="LOH">LOH</option>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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255 <option value="Wildtype">Wildtype</option>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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256 <option value="None">None</option>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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diff changeset
257 </param>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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parents: 5
diff changeset
258 <when value="Somatic" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
259 <when value="Germline" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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260 <when value="LOH" />
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261 <when value="Wildtype" />
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262 <when value="None" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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263 <when value="custom">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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264 <param name="status_custom" type="text"
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265 label="Mutation status (custom value)">
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266 <validator type="expression" message="Need a value for Mutation status">value.strip()</validator>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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267 </param>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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268 </when>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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269 <when value="expression">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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270 <param name="status_expression" type="text"
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271 label="SQL expression used to compute per-variant status"
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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272 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.">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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273 <expand macro="sanitize_query" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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274 <validator type="expression" message="Mutation status expression cannot be empty">value.strip()</validator>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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275 </param>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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276 </when>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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277 </conditional>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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278 <expand macro="sorting" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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279 </when>
5
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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280 <when value="tped">
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281 <param name="header" type="hidden" value="" />
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282 <param name="dgidb" type="hidden" value="" />
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283 <expand macro="sorting" />
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284 </when>
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285 </conditional>
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286 </section>
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287 </when>
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288 <when value="advanced">
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289 <param argument="-q" name="q" type="text" area="True" size="5x50"
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290 label="The query to be issued to the database"
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291 help="Formulate your query using SQL syntax.">
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292 <expand macro="sanitize_query" />
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293 <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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294 </param>
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295 <expand macro="gt_filter" />
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296 <expand macro="sample_filter" />
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297 <section name="oformat" title="Output format options" expanded="true">
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298 <conditional name="report">
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299 <param name="format" type="select"
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300 label="Type of report to generate">
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301 <option value="default">tabular (GEMINI default)</option>
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302 <option value="with_samples">tabular with affected samples</option>
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303 <option value="with_samples_flattened">tabular with affected samples flattened</option>
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304 <option value="with_families">tabular with affected families</option>
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305 <option value="carrier_summary">tabular with carrier summary</option>
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306 <option value="vcf">VCF (simplified)</option>
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307 <option value="json">JSON</option>
7
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308 <option value="maf">MAF (cBioportal-compatible)</option>
5
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309 <option value="tped">TPED</option>
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310 </param>
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311 <when value="default">
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312 <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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313 <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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314 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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315 <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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316 <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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317 <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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318 <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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319 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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320 <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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321 <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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322 <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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323 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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324 <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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325 <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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326 <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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327 <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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328 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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329 <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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330 <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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331 <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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332 <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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333 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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334 <when value="vcf">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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335 <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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336 <param name="dgidb" type="hidden" value="" />
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337 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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338 <when value="json">
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339 <param name="header" type="hidden" value="" />
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340 <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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341 </when>
7
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342 <when value="maf">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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343 <param name="header" type="hidden" value="--header" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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344 <param name="dgidb" type="hidden" value="" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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345 <expand macro="maf_extra_info" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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346 </when>
5
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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347 <when value="tped">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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348 <param name="header" type="hidden" value="" />
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349 <param name="dgidb" type="hidden" value="" />
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350 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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351 </conditional>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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352 </section>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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353 </when>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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354 </conditional>
0
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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diff changeset
355 </inputs>
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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356 <outputs>
5
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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357 <data name="outfile" format="tabular">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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358 <change_format>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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359 <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
iuc
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360 <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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361 </change_format>
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
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362 </data>
0
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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diff changeset
363 </outputs>
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
364 <tests>
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
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365 <test>
4
7ca6716748c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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366 <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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367 <conditional name="query">
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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368 <param name="interface" value="advanced" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
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369 <param name="q" value="select chrom,start from variants limit 10" />
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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370 </conditional>
4
7ca6716748c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 3
diff changeset
371 <output name="outfile">
7ca6716748c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 3
diff changeset
372 <assert_contents>
7ca6716748c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 3
diff changeset
373 <has_line_matching expression="chrom&#009;start" />
7ca6716748c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 3
diff changeset
374 </assert_contents>
7ca6716748c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
parents: 3
diff changeset
375 </output>
0
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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376 </test>
7
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
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377 <test>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
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378 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
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379 <conditional name="query">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
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380 <param name="interface" value="basic" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
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381 </conditional>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
382 <section name="oformat">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
383 <conditional name="report">
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
384 <param name="format" value="maf" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
385 <param name="tumor_sample_id" value="test" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
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386 </conditional>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
387 </section>
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
388 <output name="outfile" file="gemini_query_as_maf_result.tabular" />
da74170c55c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
iuc
parents: 5
diff changeset
389 </test>
0
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
390 </tests>
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
391 <help>
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
392 <![CDATA[
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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diff changeset
393 **What it does**
ab195e756e5e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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394
5
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
395 The real power in the GEMINI framework lies in the fact that all of your
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
396 genetic variants have been stored in a convenient database in the context of a
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
397 wealth of genome annotations that facilitate variant interpretation.
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 4
diff changeset
398 The expressive power of SQL allows one to pose intricate questions of one’s
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
399 variation data. This tool offers you a flexible, yet relatively easy way
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
400 to query your variants!
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
401
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 4
diff changeset
402 -----
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
403
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
404 *Building your variant query with the Basic variant query constructor*
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
405
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
406 This mode tries to break down the complexity of formulating GEMINI queries
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
407 into more easily digestable parts. In this mode, the tool also prevents you
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
408 from combining options that are incompatible or not meaningful.
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
409
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
410 *Genotype filters*
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
411
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
412 These are discussed `here
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 4
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413 <https://gemini.readthedocs.io/en/latest/content/querying.html#gt-filter-filtering-on-genotypes>`__
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
414 in the GEMINI documentation.
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
415
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 4
diff changeset
416 The tool supports regular genotype filters like::
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
417
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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parents: 4
diff changeset
418 gt.sample1 == HET and gt_depths.sample1 >= 15
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
419
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
420 , which would keep only variants for which sample 1 is a heterozygous carrier
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
421 and if the genomic position in sample1 is covered by at least 15 sequencing
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
422 reads, as well as GEMINI wildcard filters of the general form
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
423 *(COLUMN).(SAMPLE_FILTER).(RULE).(RULE_ENFORCEMENT)* like::
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
424
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
425 (gt_types).(phenotype==2).(!=HOM_REF).(all)
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
426
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
427 , which keeps only variants for which all phenotypic samples are homozygous.
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
428
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
429 *Sample filters*
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
430
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
431 Sample filters have the same format as the second component of the genotype
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
432 wildcard filters above, so::
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
433
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
434 phenotype == 2
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
435
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
436 would filter for phenotypically affected samples. In this case, however, the
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
437 filter determines, from which samples variants should be reported, i.e., here,
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
438 only variants found in phenotypically affected samples become analyzed. You can
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
439 use the ``--in`` filter to adjust the exact meaning of the sample filter.
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
440
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
441 *Region filters*
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
442
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
443 They let you restrict your analysis to parts of the genome, which can be useful
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
diff changeset
444 if you have prior knowledge of the approximate location of a variant of
cd00221d67cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
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445 interest.
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446
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447 If you specify more then one region filter, they get combined with a logical
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448 *OR*, meaning variants and genes falling in *any* of the regions are reported.
0
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449
5
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450 *Additional constraints on variants*
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451
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452 These get translated directly into the WHERE clause of an SQL query and, thus,
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453 have to be expressed in valid SQL syntax. As an example you could use::
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454
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455 is_exonic = 1 and impact_severity != 'LOW'
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456
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457 to indicate that you are only interested in exonic variants that are not of
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458 *LOW* impact severity, *i.e.*, not silent mutations.
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459
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460 Note that in SQL syntax tests for equality use a single ``=``, while genotype
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461 filters (discussed above) are following Python syntax and use ``==`` for the
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462 same purpose. Also note that non-numerical values need to be enclosed in
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463 single-quotes, *e.g.* ``'LOW'``, but numerical values must *NOT* be.
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464
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465 -----
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466
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467 *Building your query with the Advanced query constructor*
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468
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469 For the sake of simplicity, the basic mode of the tool limits your queries to
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470 the variants table of the underlying database. While this still allows many
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471 useful queries to be formulated, it prevents you from joining information from
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472 other tables (in particular, the gene_detailed table) or to query a different
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473 table directly.
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474
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475 In advanced mode, you take responsibility for formulating the complete SQL
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476 query in correct syntax, which allows you to do anything you could do with the
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477 command line tool. Beyond querying other tables, this includes changing output
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478 column names, deriving simple statistics on columns using the SQL Min, Max,
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479 Count, Avg and Sum functions, and more.
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480
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481 The price you pay for this extra flexibility is that you will have to make sure
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482 that any other tool options you set are compatible with the result of your
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483 particular query. For example, most output formats except the tabular default
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484 output of GEMINI are incompatible with non-standard queries. Choosing
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485 non-compatible options can result in them getting ignored silently, but also
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486 in tool errors, or in problems with downstream tools.
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487
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488 The chapter `Querying the GEMINI database
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489 <http://gemini.readthedocs.org/en/latest/content/querying.html>`__ of the
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490 GEMINI documentation can get you started with formulating your own queries.
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491
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492 Note that genotype filters and sample filters cannot be expressed as genuine
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493 SQL queries, so even the Advanced query constructor is offering them. Region
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494 filters and sort order of rows and columns on the other hand can be controlled
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495 through SQL queries, like in this example::
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496
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497 SELECT gene, chrom, start, end, ref, alt FROM variants WHERE chrom = 'chr1'
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498 AND start >= 10000000 and stop <= 20000000 and is_lof = 1 ORDER BY chrom,
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499 start
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500
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501 , which would report all loss-of-function variants between 10,000,000 and
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502 20,000,000 on chr1 and report the selected columns sorted on chromosome, then
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503 position.
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504
0
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505 ]]>
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506 </help>
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507 <expand macro="citations"/>
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508 </tool>