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0
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="0.10.0">gemini</requirement>
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5 <requirement type="package" version="0.1.3">grabix</requirement>
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6 <requirement type="package" version="0.2.6">tabix</requirement>
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7 <requirement type="package" version="0.1.19">samtools</requirement>
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8 <requirement type="package" version="2.19.1">bedtools</requirement>
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9 <yield />
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10 </requirements>
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11 </xml>
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12
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13 <xml name="version_command">
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14 <version_command>gemini --version</version_command>
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15 </xml>
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16
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17 <xml name="stdio">
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18 <stdio>
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19 <exit_code range="1:" />
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20 <exit_code range=":-1" />
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21 <regex match="Error:" />
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22 <regex match="Exception:" />
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23 </stdio>
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24 </xml>
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25
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26 <xml name="annotation_dir">
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27 <param name="annotation_databases" type="select" label="Choose a gemini annotation database">
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28 <options from_data_table="gemini_databases">
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29 <filter type="sort_by" column="0" />
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30 <validator type="no_options" message="No annotation database is available" />
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31 </options>
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32 </param>
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33 </xml>
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34
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35 <xml name="add_header_column">
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36 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False"
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37 label="Add a header of column names to the output" help="(--header)"/>
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38 </xml>
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39
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40 <xml name="radius">
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41 <param name="radius" type="integer" value="3" size="5" label="Set filter for Breadth-first search (BFS) in the Protein-Protein Interaction network" help="(-r)" >
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42 <validator type="in_range" min="0"/>
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43 </param>
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44 </xml>
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45 <xml name="variant_mode">
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46 <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False"
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47 label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
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48 </xml>
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49
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50 <xml name="column_filter">
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51 <conditional name="report">
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52 <param name="report_selector" type="select" label="Columns to include in the report"
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53 help="By default, this tool reports all columns in the variants table. One may choose to report only a subset of the columns.">
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54 <option value="all" selected="True">all</option>
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55 <option value="column_filter">User given columns</option>
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56 </param>
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57 <when value="all"/>
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58 <when value="column_filter">
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59 <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
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60 <option value="gene">gene</option>
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61 <option value="chrom">chrom</option>
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62 <option value="start">start</option>
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63 <option value="end">end</option>
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64 <option value="ref">ref</option>
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65 <option value="alt">alt</option>
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66 <option value="impact">impact</option>
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67 <option value="impact_severity">impact_severity</option>
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68 </param>
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69 </when>
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70 </conditional>
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71 </xml>
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72
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73 <xml name="filter">
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74 <conditional name="filter">
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75 <param name="filter_selector" type="select" label="Apply additional constraints"
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76 help="By default, this tool will report all variants regardless of their putative functional impact. In order to apply additional constraints on the variants returned, you can this optional filter.">
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77 <option value="no">No additional constraints</option>
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78 <option value="yes">Apply additional constraints</option>
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79 </param>
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80 <when value="no"/>
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81 <when value="yes">
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82 <param name="filter" type="text" size="20" label="Contraints in SQL syntax" help="Conditions applied here will become WHERE clauses in the query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'. (--filter)">
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83 <expand macro="sanitize_query" />
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84 </param>
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85 </when>
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86 </conditional>
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87 </xml>
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88
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89 <xml name="sanitize_query">
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90 <sanitizer invalid_char="">
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4
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91 <valid initial="string.printable"/>
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0
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92 </sanitizer>
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93 </xml>
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94
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4
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95 <token name="@CMDLN_SQL_FILTER_FILTER_OPTION@">
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96 #if str($filter.filter_selector) == 'yes' and $filter.filter:
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97 #import pipes
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98 --filter ${ pipes.quote( str( $filter.filter ) ) or "''" }
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99 #end if
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100 </token>
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101
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0
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102 <xml name="min_sequence_depth">
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103 <param name="d" type="integer" value="0" size="5" label="The minimum aligned sequence depth (genotype DP) required for each sample"
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104 help="default: 0 (-d)">
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105 <validator type="in_range" min="0"/>
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106 </param>
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107 </xml>
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108
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2
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109 <token name="@VERSION@">0.10.1</token>
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0
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110
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111 <token name="@CITATION@">------
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112
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113 **Citation**
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114
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115 If you use GEMINI in your research, please cite the following manuscript:
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116
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117 </token>
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118 <xml name="citations">
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119 <citations>
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120 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
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121 <yield />
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122 </citations>
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123 </xml>
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2
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124
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125 <xml name="infile">
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126 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
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127 <options options_filter_attribute="metadata.gemini_version" >
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128 <filter type="add_value" value="@VERSION@" />
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129 </options>
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130 <validator type="expression" message="This version of Gemini will only work with Gemini files that are for version @VERSION@.">value is not None and value.metadata.gemini_version == "@VERSION@"</validator>
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131 </param>
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132 </xml>
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133
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0
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134 </macros>
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