Mercurial > repos > iuc > gemini_query

annotate gemini_query.xml @ 10:37e2ac64e4f6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:22:35 +0000
parents 4e688fd8100c
children 81db0d6200da
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy1">
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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="" />
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350 <param name="dgidb" type="hidden" value="" />
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351 </when>
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352 </conditional>
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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
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parents: 6
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355 </conditional>
0
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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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359 <change_format>
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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
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parents: 6
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363 </data>
0
082448872590 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
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diff changeset
364 </outputs>
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diff changeset
365 <tests>
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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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368 <conditional name="query">
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369 <param name="interface" value="advanced" />
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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
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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
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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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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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382 </conditional>
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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383 <section name="oformat">
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iuc
parents: 7
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384 <conditional name="report">
4e688fd8100c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 5ea789e5342c3ad1afd2e0068c88f2b6dc4f7246"
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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
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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"
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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"
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parents: 7
diff changeset
388 </section>
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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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>
0
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iuc
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diff changeset
391 </tests>
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diff changeset
392 <help>
2
9dc6c42486a1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents: 0
diff changeset
393 <![CDATA[
0
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diff changeset
394 **What it does**
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395
7
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parents: 6
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396 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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parents: 6
diff changeset
397 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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parents: 6
diff changeset
398 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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parents: 6
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399 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
400 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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parents: 6
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401 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
402
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
403 -----
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
404
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
405 *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
406
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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407 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
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408 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
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409 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
410
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
411 *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
412
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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diff changeset
413 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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diff changeset
414 <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
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parents: 6
diff changeset
415 in the GEMINI documentation.
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 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
418
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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419 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
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parents: 6
diff changeset
420
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
421 , 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
422 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
423 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
424 *(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
425
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 (gt_types).(phenotype==2).(!=HOM_REF).(all)
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
427
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
428 , which keeps only variants for which all phenotypic samples are homozygous.
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
429
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 *Sample filters*
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
431
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iuc
parents: 6
diff changeset
432 Sample filters have the same format as the second component of the genotype
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
433 wildcard filters above, so::
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
434
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
435 phenotype == 2
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
436
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
437 would filter for phenotypically affected samples. In this case, however, the
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 6
diff changeset
438 filter determines, from which samples variants should be reported, i.e., here,
1cdc7f1dd605 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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439 only variants found in phenotypically affected samples become analyzed. You can
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440 use the ``--in`` filter to adjust the exact meaning of the sample filter.
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441
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442 *Region filters*
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443
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444 They let you restrict your analysis to parts of the genome, which can be useful
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445 if you have prior knowledge of the approximate location of a variant of
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446 interest.
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447
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448 If you specify more then one region filter, they get combined with a logical
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449 *OR*, meaning variants and genes falling in *any* of the regions are reported.
0
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450
7
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451 *Additional constraints on variants*
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452
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453 These get translated directly into the WHERE clause of an SQL query and, thus,
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454 have to be expressed in valid SQL syntax. As an example you could use::
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455
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456 is_exonic = 1 and impact_severity != 'LOW'
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457
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458 to indicate that you are only interested in exonic variants that are not of
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459 *LOW* impact severity, *i.e.*, not silent mutations.
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460
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461 Note that in SQL syntax tests for equality use a single ``=``, while genotype
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462 filters (discussed above) are following Python syntax and use ``==`` for the
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463 same purpose. Also note that non-numerical values need to be enclosed in
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464 single-quotes, *e.g.* ``'LOW'``, but numerical values must *NOT* be.
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465
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466 -----
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467
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468 *Building your query with the Advanced query constructor*
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469
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470 For the sake of simplicity, the basic mode of the tool limits your queries to
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471 the variants table of the underlying database. While this still allows many
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472 useful queries to be formulated, it prevents you from joining information from
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473 other tables (in particular, the gene_detailed table) or to query a different
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474 table directly.
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475
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476 In advanced mode, you take responsibility for formulating the complete SQL
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477 query in correct syntax, which allows you to do anything you could do with the
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478 command line tool. Beyond querying other tables, this includes changing output
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479 column names, deriving simple statistics on columns using the SQL Min, Max,
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480 Count, Avg and Sum functions, and more.
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481
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482 The price you pay for this extra flexibility is that you will have to make sure
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483 that any other tool options you set are compatible with the result of your
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484 particular query. For example, most output formats except the tabular default
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485 output of GEMINI are incompatible with non-standard queries. Choosing
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486 non-compatible options can result in them getting ignored silently, but also
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487 in tool errors, or in problems with downstream tools.
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488
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489 The chapter `Querying the GEMINI database
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490 <http://gemini.readthedocs.org/en/latest/content/querying.html>`__ of the
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491 GEMINI documentation can get you started with formulating your own queries.
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492
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493 Note that genotype filters and sample filters cannot be expressed as genuine
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494 SQL queries, so even the Advanced query constructor is offering them. Region
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495 filters and sort order of rows and columns on the other hand can be controlled
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496 through SQL queries, like in this example::
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497
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498 SELECT gene, chrom, start, end, ref, alt FROM variants WHERE chrom = 'chr1'
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499 AND start >= 10000000 and stop <= 20000000 and is_lof = 1 ORDER BY chrom,
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500 start
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501
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502 , which would report all loss-of-function variants between 10,000,000 and
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503 20,000,000 on chr1 and report the selected columns sorted on chromosome, then
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504 position.
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505
2
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506 ]]>
0
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507 </help>
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508 <expand macro="citations"/>
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509 </tool>