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comparison snpEff.xml @ 16:3790e16a0be0

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Add datatype: snpeffdbv4
author Jim Johnson <jj@umn.edu>
date Thu, 23 Oct 2014 05:09:26 -0500
parents fac49d7ea7d4
children 13d81e5226cd
comparison
equal deleted inserted replaced
15:fac49d7ea7d4 16:3790e16a0be0
32 -interval $intervals 32 -interval $intervals
33 #end if 33 #end if
34 #if $statsFile: 34 #if $statsFile:
35 -stats $statsFile 35 -stats $statsFile
36 #end if 36 #end if
37 #if $offset.__str__ != '': 37 #if $offset.__str__ != 'default':
38 ${offset} 38 ${offset}
39 #end if 39 #end if
40 #if $chr.__str__.strip() != '': 40 #if $chr.__str__.strip() != '':
41 -chr "$chr" 41 -chr "$chr"
42 #end if 42 #end if
43 $noLog 43 $noLog
44 #if $snpDb.genomeSrc == 'cached': 44 #if $snpDb.genomeSrc == 'cached':
45 -dataDir ${snpDb.genomeVersion.fields.path} 45 -dataDir ${snpDb.genomeVersion.fields.path}
46 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '': 46 #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != '':
47 #echo " " 47 #echo " "
48 #echo ' '.join($snpDb.extra_annotations.__str__.split(',')) 48 #echo ' '.join($snpDb.extra_annotations.__str__.split(','))
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>
116 <when value="history"> 116 <when value="history">
117 <param format="snpeffdb" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> 117 <param format="snpeffdbv4" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/>
118 <!-- From metadata --> 118 <!-- From metadata -->
119 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> 119 <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations">
120 <help>These are available for only a few genomes</help> 120 <help>These are available for only a few genomes</help>
121 <options> 121 <options>
122 <filter type="data_meta" ref="snpeff_db" key="annotation" /> 122 <filter type="data_meta" ref="snpeff_db" key="annotation" />
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="GRCh38.76" label="Snpff Version Name"/> 133 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
134 <help>http://sourceforge.net/projects/snpeff/files/databases/v4_0/</help>
135 <validator type="regex" message="A genome version name is required">\S+</validator>
136 </param>
134 </when> 137 </when>
135 </conditional> 138 </conditional>
136 139
137 <param name="udLength" type="select" label="Upstream / Downstream length"> 140 <param name="udLength" type="select" label="Upstream / Downstream length">
138 <option value="0">No upstream / downstream intervals (0 bases)</option> 141 <option value="0">No upstream / downstream intervals (0 bases)</option>
192 <option value="-no-upstream">Do not show UPSTREAM changes</option> 195 <option value="-no-upstream">Do not show UPSTREAM changes</option>
193 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option> 196 <option value="-no-utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes</option>
194 </param> 197 </param>
195 198
196 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> 199 <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">
197 <option value="" selected="true">Use default (based on input type)</option> 200 <option value="default" selected="true">Use default (based on input type)</option>
198 <option value="-0">Force zero-based positions (both input and output)</option> 201 <option value="-0">Force zero-based positions (both input and output)</option>
199 <option value="-1">Force one-based positions (both input and output)</option> 202 <option value="-1">Force one-based positions (both input and output)</option>
200 </param> 203 </param>
201 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name"> 204 <param name="chr" type="text" optionl="true" label="Text to prepend to chromosome name">
202 <help> 205 <help>