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comparison snpEff.xml @ 21:c780e3f75b3d

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Filter genome history snpeffdb by snpeff_version
author Jim Johnson <jj@umn.edu>
date Wed, 14 Jan 2015 12:03:21 -0600
parents 2e37b58fc24d
children bb0797deab78
comparison
equal deleted inserted replaced
20:7a46f9a72d3c 21:c780e3f75b3d
1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.2"> 1 <tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.3">
2 <description>Variant effect and annotation</description> 2 <description>Variant effect and annotation</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>snpEff_macros.xml</import> 5 <import>snpEff_macros.xml</import>
6 </macros> 6 </macros>
116 </param> 116 </param>
117 <when value="cached"> 117 <when value="cached">
118 <param name="genomeVersion" type="select" label="Genome"> 118 <param name="genomeVersion" type="select" label="Genome">
119 <!--GENOME DESCRIPTION--> 119 <!--GENOME DESCRIPTION-->
120 <options from_data_table="snpeffv_genomedb"> 120 <options from_data_table="snpeffv_genomedb">
121 <filter type="static_value" name="snpeff_version" value="SnpEff4.0" column="1"/> 121 <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/>
122 <filter type="unique_value" column="2" /> 122 <filter type="unique_value" column="2" />
123 </options> 123 </options>
124 </param> 124 </param>
125 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> 125 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
126 <help>These are available for only a few genomes</help> 126 <help>These are available for only a few genomes</help>
136 <filter type="unique_value" column="3" /> 136 <filter type="unique_value" column="3" />
137 </options> 137 </options>
138 </param> 138 </param>
139 </when> 139 </when>
140 <when value="history"> 140 <when value="history">
141 <param format="snpeffdbv40" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> 141 <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data">
142 <options options_filter_attribute="metadata.snpeff_version" >
143 <filter type="add_value" value="@SNPEFF_VERSION@" />
144 </options>
145 <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ Genome databases.">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
146 </param>
142 <!-- From metadata --> 147 <!-- From metadata -->
143 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> 148 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations">
144 <help>These are available for only a few genomes</help> 149 <help>These are available for only a few genomes</help>
145 <options> 150 <options>
146 <filter type="data_meta" ref="snpeff_db" key="annotation" /> 151 <filter type="data_meta" ref="snpeff_db" key="annotation" />