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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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2
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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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4
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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 <column name="value" index="0"/>
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30 <column name="dbkey" index="1"/>
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31 <column name="name" index="2"/>
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32 <column name="path" index="3"/>
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33 <filter type="sort_by" column="0" />
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34 <validator type="unspecified_build" />
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35 <validator type="no_options" message="No annotation database is available" />
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4
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36 </options>
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37 </param>
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38 </xml>
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39
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40 <xml name="add_header_column">
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41 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False"
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42 label="Add a header of column names to the output" help="(--header)"/>
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43 </xml>
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44
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45 <xml name="radius">
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46 <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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47 <validator type="in_range" min="0"/>
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48 </param>
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49 </xml>
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50 <xml name="variant_mode">
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51 <param name="variant_mode" type="boolean" truevalue="--var" falsevalue="" checked="False"
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52 label="Returns variant info (e.g. impact, biotype) for interacting genes" help="(--var)"/>
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53 </xml>
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54
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55 <xml name="column_filter">
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56 <conditional name="report">
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57 <param name="report_selector" type="select" label="Columns to include in the report"
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58 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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59 <option value="all" selected="True">all</option>
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60 <option value="column_filter">User given columns</option>
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61 </param>
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62 <when value="all"/>
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63 <when value="column_filter">
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64 <param name="columns" type="select" display="checkboxes" multiple="True" label="Choose columns to include in the report" help="(--columns)">
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65 <option value="gene">gene</option>
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66 <option value="chrom">chrom</option>
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67 <option value="start">start</option>
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68 <option value="end">end</option>
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69 <option value="ref">ref</option>
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70 <option value="alt">alt</option>
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71 <option value="impact">impact</option>
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72 <option value="impact_severity">impact_severity</option>
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73 </param>
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74 </when>
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75 </conditional>
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76 </xml>
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77
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78 <xml name="filter">
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79 <conditional name="filter">
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80 <param name="filter_selector" type="select" label="Apply additional constraints"
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81 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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82 <option value="no">No additional constraints</option>
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83 <option value="yes">Apply additional constraints</option>
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84 </param>
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85 <when value="no"/>
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86 <when value="yes">
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87 <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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88 <expand macro="sanitize_query" />
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89 </param>
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90 </when>
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91 </conditional>
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92 </xml>
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93
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94 <xml name="sanitize_query">
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95 <sanitizer invalid_char="">
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96 <valid initial="string.printable">
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97 </valid>
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98 </sanitizer>
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99 </xml>
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100
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0
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101 <xml name="min_sequence_depth">
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102 <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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103 help="default: 0 (-d)">
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104 <validator type="in_range" min="0"/>
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105 </param>
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106 </xml>
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107
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108 <token name="@VERSION@">0.10.0</token>
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109
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110 <token name="@CITATION@">------
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111
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112 **Citation**
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113
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114 If you use GEMINI in your research, please cite the following manuscript:
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115
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116 </token>
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117 <xml name="citations">
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118 <citations>
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119 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
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120 <yield />
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121 </citations>
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122 </xml>
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123 </macros>
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