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comparison snpEff.xml @ 13:4be8e0068bc3

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Update loc data to separate version 4 databases
author Jim Johnson <jj@umn.edu>
date Tue, 21 Oct 2014 14:05:27 -0500
parents 6d429d880a75
children fac49d7ea7d4
comparison
equal deleted inserted replaced
12:6d429d880a75 13:4be8e0068bc3
92 <option value="named">Named on demand</option> 92 <option value="named">Named on demand</option>
93 </param> 93 </param>
94 <when value="cached"> 94 <when value="cached">
95 <param name="genomeVersion" type="select" label="Genome"> 95 <param name="genomeVersion" type="select" label="Genome">
96 <!--GENOME DESCRIPTION--> 96 <!--GENOME DESCRIPTION-->
97 <options from_data_table="snpeff_genomedb"> 97 <options from_data_table="snpeff4_genomedb">
98 <filter type="unique_value" column="0" /> 98 <filter type="unique_value" column="0" />
99 </options> 99 </options>
100 </param> 100 </param>
101 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> 101 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
102 <help>These are available for only a few genomes</help> 102 <help>These are available for only a few genomes</help>
103 <options from_data_table="snpeff_annotations"> 103 <options from_data_table="snpeff4_annotations">
104 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 104 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
105 <filter type="unique_value" column="1" /> 105 <filter type="unique_value" column="1" />
106 </options> 106 </options>
107 </param> 107 </param>
108 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation"> 108 <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory Annotation">
109 <help>These are available for only a few genomes</help> 109 <help>These are available for only a few genomes</help>
110 <options from_data_table="snpeff_regulationdb"> 110 <options from_data_table="snpeff4_regulationdb">
111 <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> 111 <filter type="param_value" ref="genomeVersion" key="genome" column="0" />
112 <filter type="unique_value" column="1" /> 112 <filter type="unique_value" column="1" />
113 </options> 113 </options>
114 </param> 114 </param>
115 </when> 115 </when>
128 <filter type="data_meta" ref="snpeff_db" key="regulation" /> 128 <filter type="data_meta" ref="snpeff_db" key="regulation" />
129 </options> 129 </options>
130 </param> 130 </param>
131 </when> 131 </when>
132 <when value="named"> 132 <when value="named">
133 <param name="genome_version" type="text" value="GRCh37.68" label="Snpff Version Name"/> 133 <param name="genome_version" type="text" value="GRCh38.76" label="Snpff Version Name"/>
134 </when> 134 </when>
135 </conditional> 135 </conditional>
136 136
137 <param name="udLength" type="select" label="Upstream / Downstream length"> 137 <param name="udLength" type="select" label="Upstream / Downstream length">
138 <option value="0">No upstream / downstream intervals (0 bases)</option> 138 <option value="0">No upstream / downstream intervals (0 bases)</option>