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comparison gemini_load.xml @ 4:ca4449689d61 draft

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author iuc
date Mon, 25 Aug 2014 03:19:30 -0400
parents e6512af21622
children 6ab82d8ca805
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3:2ebcf5c69c5e 4:ca4449689d61
6 <import>gemini_macros.xml</import> 6 <import>gemini_macros.xml</import>
7 <token name="@BINARY@">load</token> 7 <token name="@BINARY@">load</token>
8 </macros> 8 </macros>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 gemini @BINARY@ 11 gemini
12 --annotation-dir ${annotation_databases}
13 @BINARY@
12 -v "${ infile }" 14 -v "${ infile }"
13 -t $annotation_type 15 -t $annotation_type
14 16
15 #if $ped: 17 #if $ped:
16 -p $ped 18 -p $ped
34 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)"> 36 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
35 <option value="snpEff">snpEff annotated VCF file</option> 37 <option value="snpEff">snpEff annotated VCF file</option>
36 <option value="VEP">VEP annotated VCF file</option> 38 <option value="VEP">VEP annotated VCF file</option>
37 </param> 39 </param>
38 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" /> 40 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" />
41 <expand macro="annotation_dir" />
39 42
40 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False" 43 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False"
41 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/> 44 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
42 45
43 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False" 46 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False"